Re: [galaxy-user] tophat issues

2013-12-02 Thread Jennifer Jackson

Hello Miro,

It sounds like perhaps the datatype is not being assigned correctly, 
which may mean that they quality scores are not scaled properly. To 
double check both, see the instructions in our wiki here:

http://wiki.galaxyproject.org/Support#Dataset_special_cases

If you still need help after this, please write back to share a history,

Best,

Jen
Galaxy team

On 11/29/13 5:49 AM, miroslav.sotak wrote:

To whom it may concern

I do have a problem with tophat. I can easily put fastq data to 
history and according to RNA-seq Analysis Exercise provided by 
Jeremy. We checked the type of Ascii ofset for the quality estimation. 
I tried even quality data converter set to 33 (we do have data of 
this ASCII offset from 2 different sources) but tophat for Illumina 
simply can not read the data before and even after quality format 
converter. We do not have any idea what is going on. I am logged in 
Galaxy with current email, can you check my data and is there any 
converter for quality offset?


Sincerely
Miro Sotak
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[galaxy-user] tophat issues

2013-11-30 Thread miroslav.sotak

To whom it may concern

I do have a problem with tophat. I can easily put fastq data to 
history and according to RNA-seq Analysis Exercise provided by Jeremy. 
We checked the type of Ascii ofset for the quality estimation. I tried 
even quality data converter set to 33 (we do have data of this ASCII 
offset from 2 different sources) but tophat for Illumina simply can 
not read the data before and even after quality format converter. We do 
not have any idea what is going on. I am logged in Galaxy with current 
email, can you check my data and is there any converter for quality 
offset?


Sincerely
Miro Sotak
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[galaxy-user] Tophat/Cuff parameters

2013-11-14 Thread Jennifer Jackson
Hello,

Yes, this is correct, not all parameters can be adjusted in the UI. Many
can, especially with Tophat, but not all. The list of implemented
parameters that will match the documentation is listed at the bottom of
each of these tools. The UI form itself up top may have a slightly
different human readable name, but most will include the parameter name
-r, etc.

To see all of the parameters on the forms:
1. Tophat/2 - open TopHat settings to use: Full parameter list
2. Cufflinks/merge/compare/diff - open or modify any listed on form to
see full content

This tool is in the Tool Shed (http://usegalaxy.org/toolshed), so if you
had programming resource available, then these could certainly be
modified. Development questions can go do the galaxy-...@bx.psu.edu
mailing list, but really the best place to start is in our wiki:
http://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax
http://wiki.galaxyproject.org/Tool%20Shed

It would be really helpful if you sent questions directly to the
galaxy-u...@bx.psu.edu mailing list going forward.
Thanks,

Jen
Galaxy team

On 11/14/13 1:08 PM, Irene Bassano wrote:
 Hi Jen,
 thanks a lot for your reply.

 I am trying to apply some changes to certain parameters in cufflinks.
I have read them on the manual but on galaxy are not all listed.
 is this because they have been chosen already by galaxy and set to
certain values you guys believe are optimal?
 I cannot find for example:

 Maximum genomic length allowed for a given bundle.
 Minimum intron size allowed in genome.
 Minimum average coverage required to attempt 3' trimming.

 and many others.

 I also wanted to access full parameters for Tophat and Cuffdiff...

 Any suggestion on how can I access them?

 Thanks,
 Irene
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[galaxy-user] Tophat for Illumina - built-in dog genome mislabelled

2013-10-10 Thread Court, Michael
Hi,

I minor annoyance that I had found with the current implementation of Tophat 
for Illumina (version 1.5.0) in the public usegalaxy.org site:

When you submit sequences for alignment, the dropdown list of available genomes 
gives 2 dog genome choices - BUT both are labeled the same - Dog(Canis lupus 
familiaris): canFam2.

After trial and error I found that the second (lower on the list) choice is 
actually Dog(Canis lupus familiaris): canFam3.1.

Hopefully this can be corrected at some point - maybe when the next release 
comes out from the Broad.

Michael



[cid:image002.png@01CEC5C0.75D35560]
Michael H. Court, BVSc, PhD, Diplomate ACVA
Professor and William R. Jones Endowed Chair
Individualized Medicine Program
Pharmacogenomics Laboratory
Department of Veterinary Clinical Sciences
College of Veterinary Medicine, Washington State University
100 Grimes Way, Pullman, WA 99164-6610
Office: 509-335-0817   Cell: 774-287-7082  Fax: 509-335-0880
michael.co...@vetmed.wsu.edumailto:michael.co...@vetmed.wsu.edu  
www.vetmed.wsu.eduhttp://www.vetmed.wsu.edu/



inline: image002.png___
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Re: [galaxy-user] Tophat for Illumina - built-in dog genome mislabelled

2013-10-10 Thread Jennifer Jackson

  
  
Hi Michael,

Thanks for reporting this, sounds like an older, incorrect, config
file is in place. And this can be fixed.
I will be going into the genomes area and re-verifying current
builds and other built-in data/indexes shortly. 

Thanks!

Jen
Galaxy team

On 10/10/13 1:56 PM, Court, Michael
  wrote:


  
  
  
  
  
Hi,

I minor annoyance that I had found with the
  current implementation of Tophat for Illumina (version
  1.5.0) in the public usegalaxy.org site:

When you submit sequences for alignment,
  the dropdown list of available genomes gives 2 dog genome
  choices  BUT both are labeled the same  Dog(Canis lupus
  familiaris): canFam2.

After trial and error I found that the
  second (lower on the list) choice is actually Dog(Canis lupus
  familiaris): canFam3.1.

Hopefully this can be corrected at some
  point  maybe when the next release comes out from the Broad.

Michael


  



Michael H. Court,
  BVSc, PhD, Diplomate ACVA
Professor and
  William R. Jones Endowed Chair
Individualized
  Medicine Program
Pharmacogenomics
  Laboratory
Department of
  Veterinary Clinical Sciences
College of
  Veterinary Medicine, Washington State University
100 Grimes Way,
  Pullman, WA 99164-6610
Office:
  509-335-0817 Cell: 774-287-7082 Fax: 509-335-0880
michael.co...@vetmed.wsu.edu
  www.vetmed.wsu.edu



  
  
  
  
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[galaxy-user] TopHat

2013-10-03 Thread Kumar Sankaran
Hi all, I am trying to perform TopHat for Illumina from Galaxy's Main Server, 
and it is in queue for the past 3 to 4 days. 
Is this normal? 
Thanks  Regards,Kumar.
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Re: [galaxy-user] TopHat

2013-10-03 Thread Jennifer Jackson

Hello Kumar,

The NGS queue has been down for several days now. We expect this to be 
up soon. This is related to the upgrades on the public Main server, as 
noted in the top banner. Leaving jobs queued will ensure that they are 
processed when this queue opens again.


The simplest alternatives for temporary, resource intensive, 
high-priority work include cloud Galaxy instances and potentially Other 
public Galaxies. But you can also review all options on the Choices 
wiki, including a local Galaxy, which is very simple to get started with 
(5-15 minutes) and great for smaller tasks.

http://wiki.galaxyproject.org/Cloud (Cloudman, etc.)
http://wiki.galaxyproject.org/PublicGalaxyServers
http://wiki.galaxyproject.org/BigPicture/Choices

Please know that we are very much aware of the inconvinience this is 
causing our users. The upgrades to our underlying infrastructure are 
closer now, just a few weeks out.


Thank you for your patience,

Jen
Galaxy team

On 10/2/13 11:18 PM, Kumar Sankaran wrote:


Hi all,

I am trying to perform TopHat for Illumina from Galaxy's Main Server, 
and it is in queue for the past 3 to 4 days.



Is this normal?


Thanks  Regards,

Kumar.




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[galaxy-user] Tophat Error: segment-based junction search failed with err

2013-10-02 Thread Delong, Zhou
Hello,
I don't know why I still have this problem..
I have run tophat2 with different dataset, sometimes it goes well but sometime 
I have this error.
I run only one job at a time on a virtual machine with 8G memory without using 
galaxy plateform. I tried --no-coverage-search option but it changes nothing.
Thanks.
Delong



De : Delong, Zhou
Envoyé : 27 août 2013 9:36
À : galaxy-u...@bx.psu.edu
Objet : Tophat Error: segment-based junction search failed with err

Hello,
I have run several analysis with Tophat 2 on my local instance of galaxy and I 
get this error for all of them..

segment-based junction search failed with err = 1 or -9

Here is an example of full error report:


Error in tophat:

[2013-08-23 11:56:58] Beginning TopHat run (v2.0.6)
---
[2013-08-23 11:56:58] Checking for Bowtie
  Bowtie version:2.0.2.0
[2013-08-23 11:56:58] Checking for Samtools
Samtools version:0.1.18.0
[2013-08-23 11:56:58] Checking for Bowtie index files
[2013-08-23 11:56:58] Checking for reference FASTA file
[2013-08-23 11:56:58] Generating SAM header for 
/usr/local/data/bowtie2/hg19/hg19
format:  fastq
quality scale:   phred33 (default)
[2013-08-23 11:58:04] Preparing reads
 left reads: min. length=50, max. length=50, 145339247 kept reads 
(34946 discarded)
right reads: min. length=50, max. length=50, 145340153 kept reads 
(34040 discarded)
[2013-08-23 14:16:21] Mapping left_kept_reads to genome hg19 with Bowtie2
[2013-08-24 01:04:37] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie2 
(1/2)
[2013-08-24 03:38:22] Mapping left_kept_reads_seg2 to genome hg19 with Bowtie2 
(2/2)
[2013-08-24 05:29:58] Mapping right_kept_reads to genome hg19 with Bowtie2
[2013-08-24 19:50:22] Mapping right_kept_reads_seg1 to genome hg19 with Bowtie2 
(1/2)
[2013-08-24 22:36:38] Mapping right_kept_reads_seg2 to genome hg19 with Bowtie2 
(2/2)
[2013-08-25 01:40:37] Searching for junctions via segment mapping
Coverage-search algorithm is turned on, making this step very slow
Please try running TopHat again with the option (--no-coverage-search) 
if this step takes too much time or memory.
[FAILED]
Error: segment-based junction search failed with err =-9
Collecting potential splice sites in islands


cp: cannot stat 
`/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/deletions.bed':
 No such file or directory
cp: cannot stat 
`/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/insertions.bed':
 No such file or directory

I did some research on the internet and it seems to be a memory problem to me, 
is there any solution other than rerun these jobs on a more powerful machine?

And why has Bowtie/Tophat discard different numbers of reads? What will be the 
impact? Does it means that if I don't have exact matches between the paired end 
input, it is still be possible to run the job?

Thanks,
Delong
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Re: [galaxy-user] Tophat Error: segment-based junction search failed with err

2013-10-02 Thread Jennifer Jackson

Hi Delong,

If you are mapping against a large reference genome and your datasets 
are large, 8G of memory may simply not be enough, even with omitting 
this paramater. Also, if you have set other TopHat parameters to be 
sensitive, then those can also be contributing to memory usage. 
Splitting the job up is still an option to try, as in the original post:

http://gmod.827538.n3.nabble.com/Tophat-Error-segment-based-junction-search-failed-with-err-td4035978.html

On 10/2/13 10:20 AM, Delong, Zhou wrote:

Hello,
I don't know why I still have this problem..
I have run tophat2 with different dataset, sometimes it goes well but 
sometime I have this error.
There are likely content differences between the datasets. A tool such 
as FastQC is a good one to use to investigate.
I run only one job at a time on a virtual machine with 8G memory 
without using galaxy plateform. I tried --no-coverage-search option 
but it changes nothing.
Do you mean that the tool fails on the line command? Then it will also 
fail in Galaxy using the same resources, this is expected.


If you do not want to split the job up, you could consider a Cloud Galaxy:
http://usegalaxy.org/cloud

Best,

Jen
Galaxy team

Thanks.
Delong



*De :* Delong, Zhou
*Envoyé :* 27 août 2013 9:36
*À :* galaxy-u...@bx.psu.edu
*Objet :* Tophat Error: segment-based junction search failed with err

Hello,
I have run several analysis with Tophat 2 on my local instance of 
galaxy and I get this error for all of them..


segment-based junction search failed with err = 1 or -9

Here is an example of full error report:

Error in tophat:

[2013-08-23 11:56:58] Beginning TopHat run (v2.0.6)
---
[2013-08-23 11:56:58] Checking for Bowtie
  Bowtie version:2.0.2.0
[2013-08-23 11:56:58] Checking for Samtools
Samtools version:0.1.18.0
[2013-08-23 11:56:58] Checking for Bowtie index files
[2013-08-23 11:56:58] Checking for reference FASTA file
[2013-08-23 11:56:58] Generating SAM header for 
/usr/local/data/bowtie2/hg19/hg19
format:  fastq
quality scale:   phred33 (default)
[2013-08-23 11:58:04] Preparing reads
 left reads: min. length=50, max. length=50, 145339247 kept reads 
(34946 discarded)
right reads: min. length=50, max. length=50, 145340153 kept reads 
(34040 discarded)
[2013-08-23 14:16:21] Mapping left_kept_reads to genome hg19 with Bowtie2
[2013-08-24 01:04:37] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie2 
(1/2)
[2013-08-24 03:38:22] Mapping left_kept_reads_seg2 to genome hg19 with Bowtie2 
(2/2)
[2013-08-24 05:29:58] Mapping right_kept_reads to genome hg19 with Bowtie2
[2013-08-24 19:50:22] Mapping right_kept_reads_seg1 to genome hg19 with Bowtie2 
(1/2)
[2013-08-24 22:36:38] Mapping right_kept_reads_seg2 to genome hg19 with Bowtie2 
(2/2)
[2013-08-25 01:40:37] Searching for junctions via segment mapping
Coverage-search algorithm is turned on, making this step very slow
Please try running TopHat again with the option (--no-coverage-search) 
if this step takes too much time or memory.
[FAILED]
Error: segment-based junction search failed with err =-9
Collecting potential splice sites in islands


cp: cannot stat 
`/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/deletions.bed':
 No such file or directory
cp: cannot stat 
`/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/insertions.bed':
 No such file or directory

I did some research on the internet and it seems to be a memory 
problem to me, is there any solution other than rerun these jobs on a 
more powerful machine?


And why has Bowtie/Tophat discard different numbers of reads? What 
will be the impact? Does it means that if I don't have exact matches 
between the paired end input, it is still be possible to run the job?


Thanks,
Delong


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Re: [galaxy-user] Tophat Error: segment-based junction search failed with err

2013-08-31 Thread Jennifer Jackson

Hi -

Pls see below

On 8/27/13 6:36 AM, Delong, Zhou wrote:

Hello,
I have run several analysis with Tophat 2 on my local instance of 
galaxy and I get this error for all of them..


segment-based junction search failed with err = 1 or -9

Here is an example of full error report:

Error in tophat:

[2013-08-23 11:56:58] Beginning TopHat run (v2.0.6)
---
[2013-08-23 11:56:58] Checking for Bowtie
  Bowtie version:2.0.2.0
[2013-08-23 11:56:58] Checking for Samtools
Samtools version:0.1.18.0
[2013-08-23 11:56:58] Checking for Bowtie index files
[2013-08-23 11:56:58] Checking for reference FASTA file
[2013-08-23 11:56:58] Generating SAM header for 
/usr/local/data/bowtie2/hg19/hg19
format:  fastq
quality scale:   phred33 (default)
[2013-08-23 11:58:04] Preparing reads
 left reads: min. length=50, max. length=50, 145339247 kept reads 
(34946 discarded)
right reads: min. length=50, max. length=50, 145340153 kept reads 
(34040 discarded)
[2013-08-23 14:16:21] Mapping left_kept_reads to genome hg19 with Bowtie2
[2013-08-24 01:04:37] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie2 
(1/2)
[2013-08-24 03:38:22] Mapping left_kept_reads_seg2 to genome hg19 with Bowtie2 
(2/2)
[2013-08-24 05:29:58] Mapping right_kept_reads to genome hg19 with Bowtie2
[2013-08-24 19:50:22] Mapping right_kept_reads_seg1 to genome hg19 with Bowtie2 
(1/2)
[2013-08-24 22:36:38] Mapping right_kept_reads_seg2 to genome hg19 with Bowtie2 
(2/2)
[2013-08-25 01:40:37] Searching for junctions via segment mapping
Coverage-search algorithm is turned on, making this step very slow
Please try running TopHat again with the option (--no-coverage-search) 
if this step takes too much time or memory.
[FAILED]
Error: segment-based junction search failed with err =-9
Collecting potential splice sites in islands


cp: cannot stat 
`/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/deletions.bed':
 No such file or directory
cp: cannot stat 
`/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/insertions.bed':
 No such file or directory

I did some research on the internet and it seems to be a memory 
problem to me, is there any solution other than rerun these jobs on a 
more powerful machine?
Or modify the parameters, as suggested in the error report. You might 
also be able to run the job with smaller inputs by breaking them up into 
smaller datasets (paired), but how appropriate this is depends on what 
you plan to do with the mapped data after.


And why has Bowtie/Tophat discard different numbers of reads? What 
will be the impact? Does it means that if I don't have exact matches 
between the paired end input, it is still be possible to run the job?
Not having both ends of all pairs map in every experiment is probably 
expected. And you can certainly run the mapping job without even the 
initial FASTQ inputs having exactly the same set of matched pairs (for 
example: maybe some were filtered out differently during QA steps).


The impact of having matched pairs will manifest in later steps in your 
analysis. And it depends on what you are doing how this needs to be 
manipulated upfront (or not!). Some tools, such as the Tuxedo RNA-seq 
tools, will filter down to matched pairs during later steps, such as 
Cufflinks, on their own. If doing variant calling, certain tools will 
also filter down to matched pairs or have tool form options to limit 
analysis to matched pairs - but others will expect that only matched 
pairs are input from the start. There are tools in the SAMTools tool 
group to filter/merge mapping results and tools in the Picard tool group 
to add/replace/merge labels or data results - all as needed. Each tool 
has help on the form itself, including links to the external source 
documentation.


Hopefully this helps,

Jen
Galaxy team


Thanks,
Delong


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[galaxy-user] Tophat Error: segment-based junction search failed with err

2013-08-27 Thread Delong, Zhou
Hello,
I have run several analysis with Tophat 2 on my local instance of galaxy and I 
get this error for all of them..

segment-based junction search failed with err = 1 or -9

Here is an example of full error report:


Error in tophat:

[2013-08-23 11:56:58] Beginning TopHat run (v2.0.6)
---
[2013-08-23 11:56:58] Checking for Bowtie
  Bowtie version:2.0.2.0
[2013-08-23 11:56:58] Checking for Samtools
Samtools version:0.1.18.0
[2013-08-23 11:56:58] Checking for Bowtie index files
[2013-08-23 11:56:58] Checking for reference FASTA file
[2013-08-23 11:56:58] Generating SAM header for 
/usr/local/data/bowtie2/hg19/hg19
format:  fastq
quality scale:   phred33 (default)
[2013-08-23 11:58:04] Preparing reads
 left reads: min. length=50, max. length=50, 145339247 kept reads 
(34946 discarded)
right reads: min. length=50, max. length=50, 145340153 kept reads 
(34040 discarded)
[2013-08-23 14:16:21] Mapping left_kept_reads to genome hg19 with Bowtie2
[2013-08-24 01:04:37] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie2 
(1/2)
[2013-08-24 03:38:22] Mapping left_kept_reads_seg2 to genome hg19 with Bowtie2 
(2/2)
[2013-08-24 05:29:58] Mapping right_kept_reads to genome hg19 with Bowtie2
[2013-08-24 19:50:22] Mapping right_kept_reads_seg1 to genome hg19 with Bowtie2 
(1/2)
[2013-08-24 22:36:38] Mapping right_kept_reads_seg2 to genome hg19 with Bowtie2 
(2/2)
[2013-08-25 01:40:37] Searching for junctions via segment mapping
Coverage-search algorithm is turned on, making this step very slow
Please try running TopHat again with the option (--no-coverage-search) 
if this step takes too much time or memory.
[FAILED]
Error: segment-based junction search failed with err =-9
Collecting potential splice sites in islands


cp: cannot stat 
`/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/deletions.bed':
 No such file or directory
cp: cannot stat 
`/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/insertions.bed':
 No such file or directory

I did some research on the internet and it seems to be a memory problem to me, 
is there any solution other than rerun these jobs on a more powerful machine?

And why has Bowtie/Tophat discard different numbers of reads? What will be the 
impact? Does it means that if I don't have exact matches between the paired end 
input, it is still be possible to run the job?

Thanks,
Delong
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[galaxy-user] Tophat problem on a new local instance

2013-06-11 Thread Elwood Linney
Hello, I will try this again without attachments and hope it gets on the
list.

I have installed a local instance of Galaxy as a one user in a Mac Pro
desktop.  I got some valuable help from Dannon Baker regarding how to load
large datasets into it.  However I noticed that the Upload file for this
instance would only go up to the

Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6) version of the zebrafish
assembly while where as the online version went up to the newer assembly

zebrafish assembly   Jul. 2010 (Zv9/danRER7)


While I could download newer reference genome in the program from UCSC Main
table browser
whenever the local instance offered alternatives for genomes it only went
up the earlier version
(Zv8/danRer6) (danRer6) .

I went ahead anyway, groomed 4 x 16gb datasets but when it came to Tophat,

An error occurred with this dataset: Could not determine Tophat version
/bin/sh: tophat: command not found Error indexing reference sequence
/bin/sh: bowtie-build: command not found

So minimally I have two problems that may or may not be related:

1)The Galaxy-dist that I just installed into a Mac pro does not have the
latest zebrafish assembly

2) but more importantly when I try to process groomed datasets through
Tophat and Use a built-in genome as reference it does not allow me an
option for the reference genome AND if I try to use a reference genome from
the UCSC download, it won't allow that.

So right now I am stymied--any advice?

Elwood Linney
Duke University Medical Center
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Re: [galaxy-user] Tophat problem on a new local instance

2013-06-11 Thread James Taylor
Regarding (2), have you installed bowtie and tophat on your Mac Pro?
Galaxy does not currently automatically install all of the software
needed to run tools (we are working on this through the toolshed, but
at the moment it is a manual process).

Dependencies of various tools included in the distribution are here:
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

--
James Taylor, Assistant Professor, Biology/CS, Emory University


On Tue, Jun 11, 2013 at 9:20 AM, Elwood Linney ellin...@gmail.com wrote:
 Hello, I will try this again without attachments and hope it gets on the
 list.

 I have installed a local instance of Galaxy as a one user in a Mac Pro
 desktop.  I got some valuable help from Dannon Baker regarding how to load
 large datasets into it.  However I noticed that the Upload file for this
 instance would only go up to the

 Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6) version of the zebrafish
 assembly while where as the online version went up to the newer assembly

 zebrafish assembly   Jul. 2010 (Zv9/danRER7)


 While I could download newer reference genome in the program from UCSC Main
 table browser
 whenever the local instance offered alternatives for genomes it only went up
 the earlier version
 (Zv8/danRer6) (danRer6) .

 I went ahead anyway, groomed 4 x 16gb datasets but when it came to Tophat,

 An error occurred with this dataset: Could not determine Tophat version
 /bin/sh: tophat: command not found Error indexing reference sequence
 /bin/sh: bowtie-build: command not found

 So minimally I have two problems that may or may not be related:

 1)The Galaxy-dist that I just installed into a Mac pro does not have the
 latest zebrafish assembly

 2) but more importantly when I try to process groomed datasets through
 Tophat and Use a built-in genome as reference it does not allow me an
 option for the reference genome AND if I try to use a reference genome from
 the UCSC download, it won't allow that.

 So right now I am stymied--any advice?

 Elwood Linney
 Duke University Medical Center

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Re: [galaxy-user] tophat to cuffdiff without cufflinks

2013-05-30 Thread Jennifer Jackson

Hello,

You will need to provide a GTF or GFF3 file to Cuffdiff - this is what
the tool uses as a reference base to build gene, transcript, and if
provided in the annotation attributes, transcript start site and protein
groupings to perform the differential analysis.

More details can be found here:
http://cufflinks.cbcb.umd.edu/manual.html

Our tutorial and other wiki help is linked from here, see Tools on the 
Main Server:

http://wiki.galaxyproject.org/Support#Interpreting_scientific_results

Hopefully this helps,

Jen
Galaxy team

On 5/30/13 3:15 PM, Colaneri, Alejandro Cesar wrote:

Hi

I comparing gen expression data (RNA-seq) in Arabidopsis. Different 
genotypes, different conditions. Since Arabidopsis is very well 
annotated I decided to do cuffdiff directly after tophat. However when 
building my workflow I found that the cuffdiff said a gtf file is 
necessary. Please see the picture in this email, under INPUT FORMAT. 
My question is if  I can still compare my libraries in the way I 
designed below.

// //

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Re: [galaxy-user] Tophat for Illumina is not running

2013-05-01 Thread Jennifer Jackson

Hello Lilach,

The public Main Galaxy server is very busy right now, but I do see your 
account in the queue (as I have since you first sent this email). We 
expect the processing time to improve soon. Meanwhile, the best strategy 
is to leave queued job alone and not stop/restart or they will move back 
to the end of the queue.


Or, if time is very urgent, consider a cloud version of Galaxy:
http://usegalaxy.org/cloud

Hopefully this helps to explain,

Jen
Galaxy team

On 4/30/13 12:43 AM, lilach noy wrote:

Hello,

I'm new to Galaxy so I think i'm at the right place asking this, 
though please let me know if I got it all wrong.
I sent a Tophat query on Thursday about 5 days ago and it is still 
waiting to ran (gray background).


Is to O.k? A bug? Should i keep waiting or stop everything and restart?

If this is not the address for reporting a suspicious bug, whom does 
this concern?


Thank you very much,
Lilach


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[galaxy-user] Tophat for Illumina is not running

2013-04-30 Thread lilach noy
Hello,

I'm new to Galaxy so I think i'm at the right place asking this, though
please let me know if I got it all wrong.
I sent a Tophat query on Thursday about 5 days ago and it is still waiting
to ran (gray background).

Is to O.k? A bug? Should i keep waiting or stop everything and restart?

If this is not the address for reporting a suspicious bug, whom does this
concern?

Thank you very much,
Lilach
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Re: [galaxy-user] tophat job help

2013-04-09 Thread Jennifer Jackson

Hello Dipanjana,

I am not sure if you mean that the job is actually running (yellow) or 
has been waiting in the queue (grey) during this time period (or some 
combination), but I can let you know that both processes can vary in the 
length of time they take to execute.


A job in the queue (grey) is waiting for its turn to run on the cluster. 
When Galaxy is busy, this time will be longer.


For a job that is executing (yellow), it is important to know that not 
all jobs will complete in the same time period. Factors such as the 
number and content of query sequences, the size and content of the 
target genome, and run-time parameters all contribute to how long a job 
will run.


I would expect that by now your job has completed and you know the 
outcome, and hopefully this helps to explain how the processing works. 
If time is urgent or a job exceeds the processing available on the 
public Main server, using Galaxy via the cloud is a good alternative:

http://usegalaxy.org/cloud

Best,

Jen
Galaxy team

On 4/5/13 7:45 PM, Dipanjana Datta De wrote:

Hi,
I have been running a tophat job and it seems to run forever, its now 
24 HRS . I do not understand, is it that i have done something wrong, 
the other tophat job took only 6 hrs. please help

regards,
Dipanjana

--
/*Dipanjana Datta De*/
/*Postdoctoral Fellow*/
/*Department of Pharmacology and Toxicology*/
/*Virginia Commonwealth University*/
/*Richmond, Virginia*/


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[galaxy-user] tophat job help

2013-04-05 Thread Dipanjana Datta De
Hi,
I have been running a tophat job and it seems to run forever, its now 24
HRS . I do not understand, is it that i have done something wrong, the
other tophat job took only 6 hrs. please help
regards,
Dipanjana

-- 
*Dipanjana Datta De*
*Postdoctoral Fellow*
*Department of Pharmacology and Toxicology*
*Virginia Commonwealth University*
*Richmond, Virginia*
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Re: [galaxy-user] Tophat mapping and Cufflinks output issues

2013-01-16 Thread Jeremy Goecks
Tophat should be used when mapping reads to the genome, not the transcriptome. 
Because you're mapping your reads to the transcriptome assembled via Trinity, 
Bowtie or BWA are good choices.

This also changes your downstream analyses, because Cufflinks does not work 
well on reads mapped to the transcriptome. Tools for quantitating 
transcriptome-mapped reads include RSEM and eXpress.

Good luck,
J.

 I've been using the Main Galaxy server to work on an RNA-Seq project for a 
 non-model plant, and I've noticed that my output from Tophat and Cufflinks 
 might not be as good as I'd like.  I have a reference transcriptome assembled 
 in Trinity, and it is based on the same Illumina-generated 100 bp reads I'm 
 trying to map to it.  When I use Tophat to map the reads to the reference 
 transcriptome (I have trimmed the reads and filtered the lower quality ones), 
 only about 10% of the reads actually map, so I go from 30,000,000 reads 
 before mapping to 3,000,000 that are actually mapped.  Therefore, I feel like 
 I'm losing a lot of data.  When I've changed the parameters to allow for more 
 mismatches, not many more reads seem to map, and in many cases, the Tophat 
 run fails and I receive the error message: Settings: Output files: 
 /tmp/3030460.cyberstar.psu.edu/tmpWbxTnm/dataset_5530451.*.ebwt Line rate: 
 6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one 
 in 32) FTable chars: 10 Strings: unpacked Max bucket size: def.  I've had 
 similar numbers of reads map with Bowtie by itself and BWA as well.  I've 
 also tried mapping the reads to the assembled isoforms (contigs) of the 
 transcriptome, and this results in many more reads (close to 90%) being 
 mapped.  Therefore, I figure the reads should map to the reference 
 transcriptome, and I'm not sure why this isn't happening.
 
 The other issue I've run into is that in Cuffdiff only about 4,800 genes 
 appear in the output files as being tested for differential expression.  
 There are approximately 100,000 genes in the reference transcriptome, so I 
 was thinking that there should be more than ca. 4,800 that are tested for 
 differential expression.  Should each gene be tested?  Does Cuffdiff just not 
 report some of the genes that are not differentially expressed, or is the 
 program not testing all of the genes?  
 
 If anyone can provide some help, guidance, or a suggestion, I'd greatly 
 appreciate it.  Thanks, and take care.
 
 Jim
 
 
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[galaxy-user] Tophat mapping and Cufflinks output issues

2013-01-15 Thread Jim Cohen
Hello Galaxy Users-

I've been using the Main Galaxy server to work on an RNA-Seq project for a
non-model plant, and I've noticed that my output from Tophat and Cufflinks
might not be as good as I'd like.  I have a reference transcriptome
assembled in Trinity, and it is based on the same Illumina-generated 100 bp
reads I'm trying to map to it.  When I use Tophat to map the reads to the
reference transcriptome (I have trimmed the reads and filtered the lower
quality ones), only about 10% of the reads actually map, so I go from
30,000,000 reads before mapping to 3,000,000 that are actually mapped.
 Therefore, I feel like I'm losing a lot of data.  When I've changed the
parameters to allow for more mismatches, not many more reads seem to map,
and in many cases, the Tophat run fails and I receive the error
message: *Settings:
Output files: /tmp/
3030460.cyberstar.psu.edu/tmpWbxTnm/dataset_5530451.*.ebwt Line rate: 6
(line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one
in 32) FTable chars: 10 Strings: unpacked Max bucket size: def*.  I've had
similar numbers of reads map with Bowtie by itself and BWA as well.  I've
also tried mapping the reads to the assembled isoforms (contigs) of the
transcriptome, and this results in many more reads (close to 90%) being
mapped.  Therefore, I figure the reads should map to the reference
transcriptome, and I'm not sure why this isn't happening.

The other issue I've run into is that in Cuffdiff only about 4,800 genes
appear in the output files as being tested for differential expression.
 There are approximately 100,000 genes in the reference transcriptome, so I
was thinking that there should be more than ca. 4,800 that are tested for
differential expression.  Should each gene be tested?  Does Cuffdiff just
not report some of the genes that are not differentially expressed, or is
the program not testing all of the genes?

If anyone can provide some help, guidance, or a suggestion, I'd greatly
appreciate it.  Thanks, and take care.

Jim
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Re: [galaxy-user] Tophat error.

2012-12-11 Thread Jennifer Jackson

Hello Humberto,

Are you using the public Main Galaxy instance at 
http://main.g2.bx.psu.edu (http://usegalaxy.org)? If so, and a re-run of 
the job still fails, please submit a bug report so that we can provide 
feedback.

http://wiki.galaxyproject.org/Support#Reporting_tool_errors

There was a small issue with reporting bugs the last few days that has 
since been resolved, so if you tried this earlier, and it failed, please 
try again now.


Best,

Jen
Galaxy team

On 12/9/12 9:30 AM, Humberto Boncristiani wrote:

Hi Everyone.

Somebody knows what this error message means:

An error occurred running this job:/Settings: Output files: 
/tmp/3010855.cyberstar.psu.edu/tmpU4RslD/tmpNmgc_h.*.ebwt Line rate: 
6 (line is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 
5 (one in 32) FTable chars: 10 Strings: unpacked Max bucket size: default/

/
/
/Thanks./
/
/
*Humberto.
*






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[galaxy-user] Tophat error.

2012-12-09 Thread Humberto Boncristiani
Hi Everyone.

Somebody knows what this error message means:

An error occurred running this job:Settings: Output files: 
/tmp/3010855.cyberstar.psu.edu/tmpU4RslD/tmpNmgc_h.*.ebwt Line rate: 6 (line 
is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32) 
FTable chars: 10 Strings: unpacked Max bucket size: default

Thanks.

Humberto.




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[galaxy-user] Tophat alignment statistics?

2012-12-06 Thread Wei Liao
Hi, galaxy users

How to get Tophat alignment statistics such as % of reads aligned to exon,
intron, splice junction? is there a Log file available?
How many unique and mutiple alignments?
I use Bam index, Flagstat, and Bam alignment metrix in Galaxy, but none
reported the information I need.

-- 
Wei Liao
Research Scientist,
Brentwood Biomedical Research Institute
16111 Plummer St.
Bldg 7, Rm D-122
North Hills, CA 91343
818-891-7711 ext 7645
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Re: [galaxy-user] Tophat alignment statistics?

2012-12-06 Thread Praveen Raj Somarajan

Hi Wei,

Have a look at RNASeQC which provides more than what you specified here. 
(https://confluence.broadinstitute.org/display/CGATools/RNA-SeQC)
This generates a detailed report with all relevant metrics on your RNA data.. I 
think, integrating this - a java based tool - into Galaxy should resolve your 
problem.

Hope this helps.

Raj

From: galaxy-user-boun...@lists.bx.psu.edu 
[mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Wei Liao
Sent: Friday, December 07, 2012 3:57 AM
To: galaxy-user@lists.bx.psu.edu
Subject: [galaxy-user] Tophat alignment statistics?

Hi, galaxy users

How to get Tophat alignment statistics such as % of reads aligned to exon, 
intron, splice junction? is there a Log file available?
How many unique and mutiple alignments?
I use Bam index, Flagstat, and Bam alignment metrix in Galaxy, but none 
reported the information I need.

--
Wei Liao
Research Scientist,
Brentwood Biomedical Research Institute
16111 Plummer St.
Bldg 7, Rm D-122
North Hills, CA 91343
818-891-7711 ext 7645



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[galaxy-user] tophat

2012-11-09 Thread Vevis, Christis
Hi all,

I am trying to perform tophat for illumina from the main server of galaxy and 
is in queue for 24 hours...is that normal??

Regards

Kristis Vevis, PhD Student
Cell Biology
UCL Institute of Ophthalmology
11-43 Bath Street
London
EC1V 9EL, UK
020 7608 4067

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Re: [galaxy-user] tophat

2012-11-09 Thread Dannon Baker
It isn't normal, but this can happen during periods of extremely high load like 
we're currently experiencing.  If you leave your jobs in the queue, they'll 
execute as soon as possible - don't cancel or restart your jobs as this will 
only move them to the back of the queue and delay completion.

-Dannon

On Nov 8, 2012, at 5:13 AM, Vevis, Christis christis.vevis...@ucl.ac.uk 
wrote:

 Hi all,
  
 I am trying to perform tophat for illumina from the main server of galaxy and 
 is in queue for 24 hours…is that normal??
  
 Regards
  
 Kristis Vevis, PhD Student
 Cell Biology
 UCL Institute of Ophthalmology
 11-43 Bath Street
 London
 EC1V 9EL, UK
 020 7608 4067
  
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[galaxy-user] Tophat results

2012-09-10 Thread Xiefan Fang
Dear galaxy users, 

 I aligned my RNA-seq data by using Tophat in galaxy. It generated some
Tophat deletions, Tophat insertions and Tophat splice junctions
results. These are all BED files. Does anyone know how to use/analyze these
kind of results? 

 Also, I used illumina RNA-seq. Each biological sample has 36-48 million
reads. The data for each sample were divided to 10-12 FASTQ files. When I
did the FASTQ Summary Statistics and draw boxplot for each of the
sub-file, the score value is about 9-10. Is it too low? Shall I combine the
FASTQ files for each biological sample and do the statistics again?

 At last, does anyone know how to convert a long list of zebrafish genes
(500-1000 genes) to human or mammalian orthologs? 

 

Thank you for your replies,

 Xiefan Fang

University of Florida

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[galaxy-user] Tophat settings

2012-09-06 Thread Du, Jianguang
Dear All,

I am not so sure about two Tophat settings. Please help.



1) Number of mismatches allowed in the initial read mapping

Based on the documantation, my understanding is: the reads are re-aligned to 
transcriptome/genome if the mismatches in the initial alignment is more than 
the set number (for example, the default setting is 2). In other words, the 
re-aligning will continue until the mismatches is equal to or below the set 
number. Is my understanding correct? If I am right, I have one worry: will 
Tophat stop re-aligning if the mismatch is below 2 (if I use the default 
setting). If it is true, the read will not be aligned to where it belongs to 
(with 0 mismatch).



2) Number of mismatches allowed in each segment alignment for reads mapped 
independently

Does this mean that the reads will be cut into segments if the mismatches of 
alignment is more than the set number?



Thanks in advance.

Jianguang
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Re: [galaxy-user] tophat deletions output

2012-08-22 Thread Jennifer Jackson

Hello Irene,

The file is described in the TopHat manual:
http://tophat.cbcb.umd.edu/manual.html#output

Along with the insertion files, deletions describes variation between 
the query and the reference genome at the base level (nucleotide). It 
does not describe whole transcripts or genes.


How to use this information is really up to you. This is very large and 
popular topic area with more information then I could outline in a 
simple email reply. Even in Galaxy there are many tools and data sources 
complete with descriptions and help and links to even more resources. 
More of these are under active development.


The base way to start is with some research: Galaxy searches in the Tool 
panel, Pages, Workflows, Tool Shed, the Wiki, Galaxy custom google 
searches or even just a plain Google with keywords like SNP or 
Variation or Indel or similar, alone or in combination, should get 
you going, if this interests you.


Take care,

Jen
Galaxy team

On 8/21/12 4:27 AM, i b wrote:

dear all,
how can we use the tophat deletions output?
e.g. if I want to see and conpare between two samples if a specific
gene or transcript had been deleted, how can I use this output?
is visualisation enough?

thanks,
ib
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[galaxy-user] tophat deletions output

2012-08-21 Thread i b
dear all,
how can we use the tophat deletions output?
e.g. if I want to see and conpare between two samples if a specific
gene or transcript had been deleted, how can I use this output?
is visualisation enough?

thanks,
ib
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Re: [galaxy-user] tophat output spice junction output

2012-07-29 Thread Jennifer Jackson

Hello Irene,

Please see:
http://wiki.g2.bx.psu.edu/Learn/Datatypes#Learn.2BAC8-Datatypes.Bed

The BED data format was created by UCSC:
http://genome.ucsc.edu/FAQ/FAQformat.html#format1

The TopHat manual also links to the UCSC specification:
http://tophat.cbcb.umd.edu/manual.html (scroll to TopHat Output)

Thanks!

Jen
Galaxy team

On 7/20/12 5:34 AM, i b wrote:

Hi,
where can I find an explanation of the columns in the splice junctions
output? From 7 to12 they are only numbered

thanks,
ib
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[galaxy-user] tophat output spice junction output

2012-07-20 Thread i b
Hi,
where can I find an explanation of the columns in the splice junctions
output? From 7 to12 they are only numbered

thanks,
ib
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[galaxy-user] Tophat

2012-07-10 Thread Jennifer Jackson

Hello,

Using the defaults and then testing the resulting SAM output seems to be 
what most folks are doing if they do not have access to the original 
library construction methods (e.g.  size selection). Both SAM Tools and 
Picard are in Galaxy. This is a useful post where the options are discussed:

http://www.biostars.org/post/show/16556/estimate-insert-size-in-paired-endmate-pair/

Is the data Illumina? The data source may be able to tell you if the 
adapter sequence was actually sequenced and/or if it was removed already 
or not. If present or you just suspect it is present, they would also 
have access to the Illumina fasta adapter data. You could also test with 
FastQC (before or after alignment, maybe on just a sample), then perform 
a clip based on those results, and re-run. See the tools in 'NGS: QC and 
manipulation' to perform these tasks.


Going forward, please send questions as a new thread directly to our 
mailing list at galaxy-u...@bx.psu.edu.

http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussions

Best,

Jen
Galaxy team

On 7/10/12 5:36 AM, asma.bioi...@gmail.com wrote:

Does anyone got correct answer, how to extract the correct distance between two 
pairs?

One naive question, how can I find the adapter sequence length?

Thanks!


--
Jennifer Jackson
http://galaxyproject.org



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[galaxy-user] Tophat and Bowtie2

2012-06-19 Thread Luciano Cosme
Hi,
   I installed bowtie2 and when running tophat I get the following error:

Error in tophat:

[2012-06-19 14:02:39] Beginning TopHat run (v2.0.3)
---
[2012-06-19 14:02:39] Checking for Bowtie
  Bowtie version:2.0.0.6
[2012-06-19 14:02:39] Checking for Samtools
Samtools version:0.1.18.0
[2012-06-19 14:02:39] Checking for Bowtie index files
Error: Could not find Bowtie 2 index files
(/tmp/tmpojo7bV/AgamP3.14.dna.toplevel.*.bt2)



I was wondering if I can create the index files using bowtie2 via command
line and then change the universe_wsgi.ini to:
 # Temporary files are stored in this directory.
new_file_path = database/tmp


and put the index files there. Anyway, why is it not creating the indexes?
I created links to all bowtie2 executable files. If I remove bowtie 0.12.8,
then I get a error from tophat (bowtie not installed). Is it creating the
index with bowtie 0.12.8?
Thank you.

Luciano
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Re: [galaxy-user] Tophat and Bowtie2

2012-06-19 Thread Luciano Cosme
Hi,
  I actually fixed it. I changed the wrapper in the line 105 from:
   cmd_index = 'bowtie-build %s -f %s %s' % ( space, options.own_file,
index_path )

to
   cmd_index = 'bowtie2-build %s -f %s %s' % ( space, options.own_file,
index_path )

Luciano





On Tue, Jun 19, 2012 at 3:03 PM, Luciano Cosme cosme.sim...@gmail.comwrote:


 Hi,
I installed bowtie2 and when running tophat I get the following error:

 Error in tophat:

 [2012-06-19 14:02:39] Beginning TopHat run (v2.0.3)
 ---
 [2012-06-19 14:02:39] Checking for Bowtie
 Bowtie version:2.0.0.6
 [2012-06-19 14:02:39] Checking for Samtools
   Samtools version:0.1.18.0
 [2012-06-19 14:02:39] Checking for Bowtie index files
 Error: Could not find Bowtie 2 index files 
 (/tmp/tmpojo7bV/AgamP3.14.dna.toplevel.*.bt2)



 I was wondering if I can create the index files using bowtie2 via command
 line and then change the universe_wsgi.ini to:
  # Temporary files are stored in this directory.
 new_file_path = database/tmp


 and put the index files there. Anyway, why is it not creating the indexes?
 I created links to all bowtie2 executable files. If I remove bowtie 0.12.8,
 then I get a error from tophat (bowtie not installed). Is it creating the
 index with bowtie 0.12.8?
 Thank you.

 Luciano




-- 
*Luciano Cosme*

-
PhD Candidate
Texas AM Entomology
Vector Biology Research Group
www.lcosme.com
979 845 1885
co...@tamu.edu
-
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Re: [galaxy-user] Tophat mapping

2012-04-18 Thread Jeremy Goecks
 I am wondering if these non-coding reads will be included when cufflinks 
 calculates transcript/gene expression. 

Reads will only be included if they map to assembled/known transcripts.

 And another question is:  how to know the number of reads mapped to a certain 
 exon? 

This isn't possible because a single read may map to multiple exons and/or 
transcripts. Cufflinks assigns reads probabilistically when their mapping 
cannot be uniquely determined.

See

http://cufflinks.cbcb.umd.edu/faq.html#count
http://cufflinks.cbcb.umd.edu/howitworks.html

for details.

Best,
J.___
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Re: [galaxy-user] Tophat mapping

2012-04-18 Thread Carlos Borroto
On Wed, Apr 18, 2012 at 8:37 AM, Jeremy Goecks jeremy.goe...@emory.edu wrote:
 I am wondering if these non-coding reads will be included when cufflinks
 calculates transcript/gene expression.


 Reads will only be included if they map to assembled/known transcripts.

Well it depends what transcript annotation file you pass to cuffdiff.
If you run cufflinks without using --GTF:

Tells Cufflinks to use the supplied reference annotation (a GFF file)
to estimate isoform expression. It will not assemble novel
transcripts, and the program will ignore alignments not structurally
compatible with any reference transcript.[1]

In Galaxy language, option Use Reference Annotation: with Use
reference annotation selected. Then the two other options, No or
Use reference annotation as guide, will allow cufflinks to estimate
unknown transcripts. If later you use cuffmerge to produce the
transcripts annotation from your cufflinks runs and use it for
cuffdiff, the non-coding reads will almost for sure pollute your
transcript expression estimates.

[1]http://cufflinks.cbcb.umd.edu/manual.html

Jeremy, do you have a workflow to estimate what percent of the reads
are mapping to unknown expressed regions? I would like to be able to
produce this estimate before I make a decision on which transcripts
annotation I should pass to cuffdiff. I would expect a small percent
of reads to map outside of known expressed regions, but is this number
is to big, then I would like to check for potential problems with my
library.

Regards,
Carlos
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Re: [galaxy-user] Tophat mapping

2012-04-18 Thread Jeremy Goecks
 Jeremy, do you have a workflow to estimate what percent of the reads
 are mapping to unknown expressed regions?


Here's a simple approach assuming mapped reads are in BAM format:

BAM -- SAM

SAM -- Interval

Intersect reads as interval with known annotation not allowing for any overlap.

Best,
J.
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[galaxy-user] Tophat paired end read

2012-04-09 Thread 杨继文
 Hi all,
I have paired end RNA-Seq reads ( Illumina Hiseq 2000) in seperate files. 
Before mapping, I need to trim the reads.

My questions is : Do I have to join pair end reads before timming, and then 
split again for Tophat???

Lookiong forward to your answers.

Thanks

Jiwen
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Re: [galaxy-user] Tophat paired end read

2012-04-09 Thread Jennifer Jackson

Hello Jiwen,

No, you do not need to join the files for the quality processing.

Hopefully this helps!

Best,

Jen
Galaxy team

On 4/9/12 9:14 AM, 杨继文 wrote:

Hi all,
I have paired end RNA-Seq reads ( Illumina Hiseq 2000) in seperate
files. Before mapping, I need to trim the reads.

My questions is : Do I have to join pair end reads before timming, and
then split again for Tophat???

Lookiong forward to your answers.

Thanks

Jiwen




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Re: [galaxy-user] Tophat paired end read

2012-04-09 Thread Carlos Borroto
Jiwen, I wonder if you are thinking about the situation where you
could be discarding reads that are to short after trimming?. In that
case you could be getting the two files out of sync. If this is the
case, I think you do need to join the files first, do the trimming and
then take them apart again.


Regards,
Carlos

On Mon, Apr 9, 2012 at 1:25 PM, Jennifer Jackson j...@bx.psu.edu wrote:
 Hello Jiwen,

 No, you do not need to join the files for the quality processing.

 Hopefully this helps!

 Best,

 Jen
 Galaxy team


 On 4/9/12 9:14 AM, 杨继文 wrote:

 Hi all,
 I have paired end RNA-Seq reads ( Illumina Hiseq 2000) in seperate
 files. Before mapping, I need to trim the reads.

 My questions is : Do I have to join pair end reads before timming, and
 then split again for Tophat???

 Lookiong forward to your answers.

 Thanks

 Jiwen




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[galaxy-user] Tophat error

2012-03-14 Thread David Matthews

Hi,

JUst running a TopHat job which returned the following error:

Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect 
/local/tmp5Ywx45/dataset_942  ./tophat_out/tmp/dataset_942.fa
[Tue Mar 13 12:45:08 2012] Checking for Bowtie
Bowtie version:  0.12.7.0
[Tue Mar 13 12:45:08 2012] Checking for Samtools
Samtools Version: 0.1.18
[Tue Mar 13 12:45:08 2012] Generating SAM header for 
/local/tmp5Ywx45/dataset_942
format:  fastq
quality scale:   phred33 (default)
[Tue Mar 13 12:45:21 2012] Preparing reads
left reads: min. length=56, count=29523921
right reads: min. length=56, count=29543412
[Tue Mar 13 13:07:54 2012] Mapping left_kept_reads against dataset_942 with 
Bowtie 
[Tue Mar 13 13:45:26 2012] Processing bowtie hits
[Tue Mar 13 14:11:28 2012] Mapping left_kept_reads_seg1 against dataset_942 
with Bowtie (1/2)
[Tue Mar 13 14:43:27 2012] Mapping left_kept_reads_seg2 against dataset_942 
with Bowtie (2/2)
[Tue Mar 13 14:57:50 2012] Mapping right_kept_reads against dataset_942 with 
Bowtie 
[Tue Mar 13 15:37:46 2012] Processing bowtie hits
[Tue Mar 13 16:04:28 2012] Mapping right_kept_reads_seg1 against dataset_942 
with Bowtie (1/2)
[Tue Mar 13 16:37:18 2012] Mapping right_kept_reads_seg2 against dataset_942 
with Bowtie (2/2)
[Tue Mar 13 16:50:40 2012] Searching for junctions via segment mapping
Traceback (most recent call last):
  File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3063, in module
sys.exit(main())
  File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3029, in main
user_supplied_deletions)
  File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 2681, in 
spliced_alignment
[maps[initial_reads[left_reads]].unspliced_bwt, 
maps[initial_reads[left_reads]].seg_maps[-1]],
TypeError: list indices must be integers, not str
Does anyone know what this kind of error is?

Best Wishes,
David.

__
Dr David A. Matthews

Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Bristol.
BS8 1TD
U.K.

Tel. +44 117 3312058
Fax. +44 117 3312091

d.a.matth...@bristol.ac.uk






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[galaxy-user] Tophat error

2012-03-14 Thread David Matthews
Hi,

JUst running a TopHat job which returned the following error:

Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect 
/local/tmp5Ywx45/dataset_942  ./tophat_out/tmp/dataset_942.fa
[Tue Mar 13 12:45:08 2012] Checking for Bowtie
Bowtie version:  0.12.7.0
[Tue Mar 13 12:45:08 2012] Checking for Samtools
Samtools Version: 0.1.18
[Tue Mar 13 12:45:08 2012] Generating SAM header for 
/local/tmp5Ywx45/dataset_942
format:  fastq
quality scale:   phred33 (default)
[Tue Mar 13 12:45:21 2012] Preparing reads
left reads: min. length=56, count=29523921
right reads: min. length=56, count=29543412
[Tue Mar 13 13:07:54 2012] Mapping left_kept_reads against dataset_942 with 
Bowtie 
[Tue Mar 13 13:45:26 2012] Processing bowtie hits
[Tue Mar 13 14:11:28 2012] Mapping left_kept_reads_seg1 against dataset_942 
with Bowtie (1/2)
[Tue Mar 13 14:43:27 2012] Mapping left_kept_reads_seg2 against dataset_942 
with Bowtie (2/2)
[Tue Mar 13 14:57:50 2012] Mapping right_kept_reads against dataset_942 with 
Bowtie 
[Tue Mar 13 15:37:46 2012] Processing bowtie hits
[Tue Mar 13 16:04:28 2012] Mapping right_kept_reads_seg1 against dataset_942 
with Bowtie (1/2)
[Tue Mar 13 16:37:18 2012] Mapping right_kept_reads_seg2 against dataset_942 
with Bowtie (2/2)
[Tue Mar 13 16:50:40 2012] Searching for junctions via segment mapping
Traceback (most recent call last):
  File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3063, in module
sys.exit(main())
  File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3029, in main
user_supplied_deletions)
  File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 2681, in 
spliced_alignment
[maps[initial_reads[left_reads]].unspliced_bwt, 
maps[initial_reads[left_reads]].seg_maps[-1]],
TypeError: list indices must be integers, not str
Does anyone know what this kind of error is?


Best Wishes,
David.

__
Dr David A. Matthews

Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Bristol.
BS8 1TD
U.K.

Tel. +44 117 3312058
Fax. +44 117 3312091

d.a.matth...@bristol.ac.uk






___
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at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
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[galaxy-user] Tophat error

2012-03-14 Thread David Matthews
Hi,

JUst running a TopHat job which returned the following error:

Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect 
/local/tmp5Ywx45/dataset_942  ./tophat_out/tmp/dataset_942.fa
[Tue Mar 13 12:45:08 2012] Checking for Bowtie
Bowtie version:  0.12.7.0
[Tue Mar 13 12:45:08 2012] Checking for Samtools
Samtools Version: 0.1.18
[Tue Mar 13 12:45:08 2012] Generating SAM header for 
/local/tmp5Ywx45/dataset_942
format:  fastq
quality scale:   phred33 (default)
[Tue Mar 13 12:45:21 2012] Preparing reads
left reads: min. length=56, count=29523921
right reads: min. length=56, count=29543412
[Tue Mar 13 13:07:54 2012] Mapping left_kept_reads against dataset_942 with 
Bowtie 
[Tue Mar 13 13:45:26 2012] Processing bowtie hits
[Tue Mar 13 14:11:28 2012] Mapping left_kept_reads_seg1 against dataset_942 
with Bowtie (1/2)
[Tue Mar 13 14:43:27 2012] Mapping left_kept_reads_seg2 against dataset_942 
with Bowtie (2/2)
[Tue Mar 13 14:57:50 2012] Mapping right_kept_reads against dataset_942 with 
Bowtie 
[Tue Mar 13 15:37:46 2012] Processing bowtie hits
[Tue Mar 13 16:04:28 2012] Mapping right_kept_reads_seg1 against dataset_942 
with Bowtie (1/2)
[Tue Mar 13 16:37:18 2012] Mapping right_kept_reads_seg2 against dataset_942 
with Bowtie (2/2)
[Tue Mar 13 16:50:40 2012] Searching for junctions via segment mapping
Traceback (most recent call last):
  File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3063, in module
sys.exit(main())
  File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3029, in main
user_supplied_deletions)
  File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 2681, in 
spliced_alignment
[maps[initial_reads[left_reads]].unspliced_bwt, 
maps[initial_reads[left_reads]].seg_maps[-1]],
TypeError: list indices must be integers, not str
Does anyone know what this kind of error is?

Best Wishes,
David.



__
Dr David A. Matthews

Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Bristol.
BS8 1TD
U.K.

Tel. +44 117 3312058
Fax. +44 117 3312091

d.a.matth...@bristol.ac.uk






___
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Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
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please use the interface at:

  http://lists.bx.psu.edu/

Re: [galaxy-user] Tophat error

2012-03-14 Thread Jennifer Jackson

Hi David,

You question has posted to the list now and we will be getting back to 
you. It didn't post immediately due to some mail mailman server issues here.


This looks like a problem that came up on a local instance. Because of 
that, I am going to send this over to the galaxy-...@bx.psu.edu mailing 
list. At first glance, this appears to be a problem with the NGS genome 
indexes used for the target genome. These are the instructions you 
followed?
http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup (Bowtie indexes are 
used for TopHat)


We will be looking at this more later today, but I wanted to get back to 
you, so you that you know that this doesn't need to be posted again.


Thanks!

Jen
Galaxy team

On 3/14/12 6:48 AM, David Matthews wrote:

Hi,

JUst running a TopHat job which returned the following error:

Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect 
/local/tmp5Ywx45/dataset_942  ./tophat_out/tmp/dataset_942.fa
[Tue Mar 13 12:45:08 2012] Checking for Bowtie
Bowtie version:  0.12.7.0
[Tue Mar 13 12:45:08 2012] Checking for Samtools
Samtools Version: 0.1.18
[Tue Mar 13 12:45:08 2012] Generating SAM header for 
/local/tmp5Ywx45/dataset_942
format:  fastq
quality scale:   phred33 (default)
[Tue Mar 13 12:45:21 2012] Preparing reads
left reads: min. length=56, count=29523921
right reads: min. length=56, count=29543412
[Tue Mar 13 13:07:54 2012] Mapping left_kept_reads against dataset_942 with 
Bowtie
[Tue Mar 13 13:45:26 2012] Processing bowtie hits
[Tue Mar 13 14:11:28 2012] Mapping left_kept_reads_seg1 against dataset_942 
with Bowtie (1/2)
[Tue Mar 13 14:43:27 2012] Mapping left_kept_reads_seg2 against dataset_942 
with Bowtie (2/2)
[Tue Mar 13 14:57:50 2012] Mapping right_kept_reads against dataset_942 with 
Bowtie
[Tue Mar 13 15:37:46 2012] Processing bowtie hits
[Tue Mar 13 16:04:28 2012] Mapping right_kept_reads_seg1 against dataset_942 
with Bowtie (1/2)
[Tue Mar 13 16:37:18 2012] Mapping right_kept_reads_seg2 against dataset_942 
with Bowtie (2/2)
[Tue Mar 13 16:50:40 2012] Searching for junctions via segment mapping
Traceback (most recent call last):
   File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3063, inmodule
 sys.exit(main())
   File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3029, in main
 user_supplied_deletions)
   File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 2681, in 
spliced_alignment
 [maps[initial_reads[left_reads]].unspliced_bwt, 
maps[initial_reads[left_reads]].seg_maps[-1]],
TypeError: list indices must be integers, not str

Does anyone know what this kind of error is?

Best Wishes,
David.



__
Dr David A. Matthews

Senior Lecturer in Virology
Room E49
Department of Cellular and Molecular Medicine,
School of Medical Sciences
University Walk,
University of Bristol
Bristol.
BS8 1TD
U.K.

Tel. +44 117 3312058
Fax. +44 117 3312091

d.a.matth...@bristol.ac.uk mailto:d.a.matth...@bristol.ac.uk








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at usegalaxy.org.  Please keep all replies on the list by
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Re: [galaxy-user] Tophat error

2012-03-14 Thread David Matthews
Hi,

Thanks for the reply, sorry about the multiple posts - it kept getting bounced 
so I resubmitted the question. We seem to be having real problems with our 
local install so I'll add it to the list...!

Cheers
David



On 14 Mar 2012, at 18:10, Jennifer Jackson wrote:

 Hi David,
 
 You question has posted to the list now and we will be getting back to you. 
 It didn't post immediately due to some mail mailman server issues here.
 
 This looks like a problem that came up on a local instance. Because of that, 
 I am going to send this over to the galaxy-...@bx.psu.edu mailing list. At 
 first glance, this appears to be a problem with the NGS genome indexes used 
 for the target genome. These are the instructions you followed?
 http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup (Bowtie indexes are used 
 for TopHat)
 
 We will be looking at this more later today, but I wanted to get back to you, 
 so you that you know that this doesn't need to be posted again.
 
 Thanks!
 
 Jen
 Galaxy team
 
 On 3/14/12 6:48 AM, David Matthews wrote:
 Hi,
 
 JUst running a TopHat job which returned the following error:
 
 Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect 
 /local/tmp5Ywx45/dataset_942  ./tophat_out/tmp/dataset_942.fa
 [Tue Mar 13 12:45:08 2012] Checking for Bowtie
  Bowtie version:  0.12.7.0
 [Tue Mar 13 12:45:08 2012] Checking for Samtools
  Samtools Version: 0.1.18
 [Tue Mar 13 12:45:08 2012] Generating SAM header for 
 /local/tmp5Ywx45/dataset_942
  format:  fastq
  quality scale:   phred33 (default)
 [Tue Mar 13 12:45:21 2012] Preparing reads
  left reads: min. length=56, count=29523921
  right reads: min. length=56, count=29543412
 [Tue Mar 13 13:07:54 2012] Mapping left_kept_reads against dataset_942 with 
 Bowtie
 [Tue Mar 13 13:45:26 2012] Processing bowtie hits
 [Tue Mar 13 14:11:28 2012] Mapping left_kept_reads_seg1 against dataset_942 
 with Bowtie (1/2)
 [Tue Mar 13 14:43:27 2012] Mapping left_kept_reads_seg2 against dataset_942 
 with Bowtie (2/2)
 [Tue Mar 13 14:57:50 2012] Mapping right_kept_reads against dataset_942 with 
 Bowtie
 [Tue Mar 13 15:37:46 2012] Processing bowtie hits
 [Tue Mar 13 16:04:28 2012] Mapping right_kept_reads_seg1 against dataset_942 
 with Bowtie (1/2)
 [Tue Mar 13 16:37:18 2012] Mapping right_kept_reads_seg2 against dataset_942 
 with Bowtie (2/2)
 [Tue Mar 13 16:50:40 2012] Searching for junctions via segment mapping
 Traceback (most recent call last):
   File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3063, inmodule
 sys.exit(main())
   File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 3029, in main
 user_supplied_deletions)
   File /gpfs/cluster/isys/galaxy/Software/bin/tophat, line 2681, in 
 spliced_alignment
 [maps[initial_reads[left_reads]].unspliced_bwt, 
 maps[initial_reads[left_reads]].seg_maps[-1]],
 TypeError: list indices must be integers, not str
 
 Does anyone know what this kind of error is?
 
 Best Wishes,
 David.
 
 
 
 __
 Dr David A. Matthews
 
 Senior Lecturer in Virology
 Room E49
 Department of Cellular and Molecular Medicine,
 School of Medical Sciences
 University Walk,
 University of Bristol
 Bristol.
 BS8 1TD
 U.K.
 
 Tel. +44 117 3312058
 Fax. +44 117 3312091
 
 d.a.matth...@bristol.ac.uk mailto:d.a.matth...@bristol.ac.uk
 
 
 
 
 
 
 
 
 ___
 The Galaxy User list should be used for the discussion of
 Galaxy analysis and other features on the public server
 at usegalaxy.org.  Please keep all replies on the list by
 using reply all in your mail client.  For discussion of
 local Galaxy instances and the Galaxy source code, please
 use the Galaxy Development list:
 
   http://lists.bx.psu.edu/listinfo/galaxy-dev
 
 To manage your subscriptions to this and other Galaxy lists,
 please use the interface at:
 
   http://lists.bx.psu.edu/


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Re: [galaxy-user] Tophat Mean Inner Distance between Mate Pairs

2012-03-13 Thread Jennifer Jackson

Hi JIwen,

As the seqanswers thread shows, there is some debate about this. One of 
the last posts there makes the most sense - where fragment length is 
defined as the total genome bases covered by the aligned paired 
sequences: tip of 5' start, through the gap, to the very 3' tail end and 
where mean inner distance is the gap in the middle (between the paired 
seqs) where there is no alignment. This could be tested with smaller 
samples of data and compared to your fragment selection, to see how it 
matches up. But, for a definitive answer, asking the tool authors is the 
best bet. The contact information is: tophat.cuffli...@gmail.com


If you are given a reply that explains the calculation, it would be 
great if the TopHat documentation itself were updated.

http://tophat.cbcb.umd.edu/manual.html

And we would be very glad to hear of the details, so that here at Galaxy 
we could add the information to our RNA-seq help and the searchable 
mailing list archives.


Great question! If we find out ourselves meanwhile, an update will be 
posted back here to the mailing list,


Best,

Jen
Galaxy team

On 3/6/12 12:23 PM, 杨继文 wrote:

Hi all,
When mapping pair end RNA-seq reads using tophat, we need to type in
Mean Inner Distance between Mate Pairs. In galaxy, we can read the
following information:

This is the expected (mean) inner distance between mate pairs. For, example, 
for paired end runs with fragments
  selected at 300bp, where each end is 50bp, you should set -r to be 200. There 
is no default, and this parameter
  is required for paired end runs.

I think the size of fragment (here 300bp) includes not only the length of pair 
end reads, but also the length of adaptors. so, maybe the Mean Inner Distance 
between Mate Pairs should be : fragment length - pair end read length - adaptor 
length. Am I right? or did I miss something?

Is it a must to type in the accurate value?

Looking forward to your reply

JIwen





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___
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Re: [galaxy-user] Tophat

2012-03-09 Thread Jennifer Jackson

Hello Jiwen,

The tool NGS: Picard (beta) - SAM/BAM Alignment Summary Metrics gives 
a nice set of statistics for paired end data.


Hopefully this helps,

Best,

Jen
Galaxy team

On 3/7/12 12:35 AM, 杨继文 wrote:

Dear all,
This might be a silly question, but I couldn't figure it out by myself
:-((. Could you please tell me how I can find out how many reads have
been mapped to the genome after running Tophat for pair end RNA seq data?
Thanks in advance.
JIwen




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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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[galaxy-user] Tophat

2012-03-07 Thread 杨继文
Dear all,
 
This might be a silly question, but I couldn't figure it out by myself :-((. 
Could you please tell me how I can find out  how many reads have been mapped to 
the genome after running Tophat for pair end RNA seq data?
 
Thanks in advance.
 
JIwen___
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[galaxy-user] Tophat Mean Inner Distance between Mate Pairs

2012-03-06 Thread 杨继文
Hi all,
 
When mapping pair end RNA-seq reads using tophat, we need to type in Mean 
Inner Distance between Mate Pairs.  In galaxy, we can read the following 
information:
This is the expected (mean) inner distance between mate pairs. For, example, 
for paired end runs with fragments
 selected at 300bp, where each end is 50bp, you should set -r to be 200. There 
is no default, and this parameter
 is required for paired end runs.
I think the size of fragment (here 300bp) includes not only the length of pair 
end reads, but also the length of adaptors. so, maybe the Mean Inner Distance 
between Mate Pairs should be : fragment length - pair end read length - adaptor 
length. Am I right? or did I miss something?  
Is it a must to type in the accurate value?
Looking forward to your reply
JIwen ___
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using reply all in your mail client.  For discussion of
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Re: [galaxy-user] Tophat Mean Inner Distance between Mate Pairs

2012-03-06 Thread Carlos Borroto
Hi Jiwen,

This is a subject that has me very confused too. This thread at
seqanswer didn't help much either:
http://seqanswers.com/forums/showthread.php?t=8730

But it does have some good comments on the subject.

I did try using the two possible options I can think of:
fragment length - pair end read length - adaptor length

And:
fragment length - pair end read length

With the latter I get around 10% increase on properly paired reads. I
wonder if Tophat internally takes into account the adapters.

Still, it would be nice to get a definitive answer in this subject.

Regards,
Carlos

2012/3/6 杨继文 jiwenyang0...@126.com:
 Hi all,

 When mapping pair end RNA-seq reads using tophat, we need to type in Mean
 Inner Distance between Mate Pairs.  In galaxy, we can read the following
 information:

 This is the expected (mean) inner distance between mate pairs. For, example,
 for paired end runs with fragments
  selected at 300bp, where each end is 50bp, you should set -r to be 200.
 There is no default, and this parameter
  is required for paired end runs.

 I think the size of fragment (here 300bp) includes not only the length of
 pair end reads, but also the length of adaptors. so, maybe the Mean Inner
 Distance between Mate Pairs should be : fragment length - pair end read
 length - adaptor length. Am I right? or did I miss something?

 Is it a must to type in the accurate value?

 Looking forward to your reply

 JIwen




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[galaxy-user] TopHat version in GALAXY

2012-02-27 Thread Genaro Pimienta
Dear all:
I have GALAXY installed in a UNIX server. BOWTIE works fine but TOPHAT and
CUFFDIFF crash upon starting.
In the case of TOPHAT, I noticed that GALAXY has a 1.5.0 version
integrated, while the TOPHAT website claims the latest version is 1.4.1.
My question is which are the best/appropiate TOPHAT and CUFFDIFF versions?
The error message I get is TOPHAT not recognized.
Any other suggestions?
Thanks,
G.
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Re: [galaxy-user] TopHat version in GALAXY

2012-02-27 Thread Jeremy Goecks
Genaro,

 My question is which are the best/appropiate TOPHAT and CUFFDIFF versions?

Galaxy wrapper versions do not match tool versions. The tag 'requirements' will 
eventually be used to specify versions, but this work is not yet complete.

You should use Tophat v1.4.0 or 1.4.1 and Cufflinks v1.3.0 for now.

 The error message I get is TOPHAT not recognized.

To solve this problem, you'll need to install Tophat and add it to your Galaxy 
user's path

 Any other suggestions?

Please send questions about local Galaxy installs to galaxy-dev rather than 
galaxy-user; galaxy-user is for questions about how to use Galaxy for 
bioinformatics analyses.

Thanks,
J.
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Re: [galaxy-user] TopHat version in GALAXY

2012-02-27 Thread Jennifer Jackson

Hi Genaro,

For reference, these are the tool version recommended for use with local 
installs:

http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies

for Bowtie, the supported version is 0.12.7
for Tophat, the supported versions are 1.3.3-1.4.0
for Cufflinks/merge/diff, the supported version is 1.3.0

Using a supported version of these tools should resolve the issues you 
are having. However, if you continue to have problems. please feel free 
to write back. The best list to send questions about local installs to 
is the galaxy-...@bx.psu.edu mailing list:

http://wiki.g2.bx.psu.edu/Support#Mailing_Lists

Best,
Jen
Galaxy team

On 2/25/12 7:27 AM, Genaro Pimienta wrote:

Dear all:
I have GALAXY installed in a UNIX server. BOWTIE works fine but TOPHAT
and CUFFDIFF crash upon starting.
In the case of TOPHAT, I noticed that GALAXY has a 1.5.0 version
integrated, while the TOPHAT website claims the latest version is 1.4.1.
My question is which are the best/appropiate TOPHAT and CUFFDIFF versions?
The error message I get is TOPHAT not recognized.
Any other suggestions?
Thanks,
G.


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[galaxy-user] Tophat settings

2012-02-08 Thread Jack Colicchio
In the new version of tophat they allow for over 3 mismatches in the initial 
alignment, however your server still gives an error if you attempt to move this 
over 3.  This is problematic for trying to map RNAseq reads where there is 
moderate divergence between the RNA and the reference genome.


Jack


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Re: [galaxy-user] Tophat settings

2012-02-08 Thread Jeremy Goecks
You're correct Jack. I've modified the Tophat wrapper to remove this 
restriction; the change will make its way to our public server soon.

Best,
J.

On Feb 8, 2012, at 1:27 PM, Jack Colicchio wrote:

 In the new version of tophat they allow for over 3 mismatches in the initial 
 alignment, however your server still gives an error if you attempt to move 
 this over 3.  This is problematic for trying to map RNAseq reads where there 
 is moderate divergence between the RNA and the reference genome.
 
 
 Jack
 
 
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[galaxy-user] Tophat

2012-02-03 Thread 杨继文
Dear all,
Today I used Tophat to map the reads from RNA-Seq, and had a look at the 
results using visaulization function. In some regions I can see splice 
junctions calculated by Tophat, but I don't see any reads mapping to this 
region. Is this a bit strange? I thought splice junction is calculated from 
the mapped reads.
However, I think cufflinks only uses accepted hits as input, maybe it is not 
a big problem that splice junction' is not accurate.
Am I right? Was there something wrong when I mapped my reads with tophat?
Hope you can help me figure it out.
Looking forward to hearing from you.
Jiwen
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Re: [galaxy-user] Tophat

2012-02-03 Thread Jennifer Jackson

Hello Jiwen,

It is possible to view both the TopHat and Cufflinks output together in 
Trackster. Are you doing this?


Are you seeing that reads/transcripts are spanning the splice regions 
(align to one side, span the gap, then align to the other side)? This is 
what would be expected for RNA-seq data.


It might help to import a known transcript track from UCSC or Biomart 
and visualize that, to get a better understanding of how genomic 
features are represented in the Trackster UI.


If you have an error dataset from an RNA-seq tool, you can send in a bug 
report, but that doesn't seem to be the case. Rather, there is a 
question about how the calculation are done. For cases like that, the 
tool authors might be the best source for help. Contact info is in this 
wiki link Example: unexpected results with RNA-seq analysis tools.

http://wiki.g2.bx.psu.edu/Support#Unexpected_scientific_result

Hopefully this helps,

Best,

Jen
Galaxy team

On 2/3/12 7:24 AM, 杨继文 wrote:

Dear all,
Today I used Tophat to map the reads from RNA-Seq, and had a look at the
results using visaulization function. In some regions I can see splice
junctions calculated by Tophat, but I don't see any reads mapping to
this region. Is this a bit strange? I thought splice junction is
calculated from the mapped reads.
However, I think cufflinks only uses accepted hits as input, maybe it
is not a big problem that splice junction' is not accurate.
Am I right? Was there something wrong when I mapped my reads with tophat?
Hope you can help me figure it out.
Looking forward to hearing from you.
Jiwen




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Re: [galaxy-user] Tophat jobs not starting

2011-12-19 Thread Nate Coraor
On Dec 14, 2011, at 11:19 AM, Magdalena Strzelecka wrote:

 Hi, 
 
 I have submitted some jobs to Tophat, but they have not started since 
 yesterday (Dec 13th); i.e they were in a queue for 12 hrs. I have 
 re-submitted everything again (2 jobs), but the same situation is happening. 
 Is there some issue with Tophat at the moment?

Hi Magdalena,

This was due to a problem with the cluster Galaxy uses to run certain jobs. 
This was resolved early last week, although there may have been a few 
intermittent problems after that time. If tophat still has not run 
successfully, please let us know.

Our sincere apologies for the inconvenience,

Best,
--nate

 Thanks.
 M.
 
 --
 Magdalena Strzelecka, PhD
 
 Heald Lab
 University of California, Berkeley
 Department of Molecular  Cell Biology
 315 Life Sciences Addition # 3200
 Berkeley, CA 94720-3200
 
 phone: (510) 643-5002
 fax: (510) 643-6791
 e-mail: strzele...@berkeley.edu
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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[galaxy-user] Tophat jobs not starting

2011-12-14 Thread Magdalena Strzelecka

Hi,

I have submitted some jobs to Tophat, but they have not started since  
yesterday (Dec 13th); i.e they were in a queue for 12 hrs. I have re- 
submitted everything again (2 jobs), but the same situation is  
happening. Is there some issue with Tophat at the moment?

Thanks.
M.

--
Magdalena Strzelecka, PhD

Heald Lab
University of California, Berkeley
Department of Molecular  Cell Biology
315 Life Sciences Addition # 3200
Berkeley, CA 94720-3200

phone: (510) 643-5002
fax: (510) 643-6791
e-mail: strzele...@berkeley.edu















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[galaxy-user] TopHat

2011-12-07 Thread Jennifer Jackson

Hello Tao,

The tools in the group NGS: Picard (beta) - QC/Metrics for sam/bam 
can generate statistics, in particular the tool SAM/BAM Alignment 
Summary Metrics.


Another choice is NGS: SAM Tools - flagstat.

If more statistics are needed, then starting with the original FASTQ and 
the mapping result SAM file, the tools in Text Manipulation, Filter 
and Sort, and Join, and Subtract and Group can be used in custom 
combinations.


This question was almost missed. I was able to locate, format, and send 
as a new thread to the appropriate mailing list. Hopefully this reply 
helps or you have already found the tools above.


Please help us to track new questions and provide prompt help by sending 
tool and data questions:


1 - to either galaxy-u...@bx.psu.edu or galaxy-...@bx.psu.edu, which are 
best for most questions. sending to galaxy-b...@bx.psu.edu is mainly 
reserved for UI bug reports (green bug icon for failed datasets) or for 
sending shared links to private data.

http://wiki.g2.bx.psu.edu/Support#Public_mailing_list_Q_.26_A_discussions

2 - with the to as the mailing list address galaxy-u...@bx.psu.edu. 
When a brand new question is sent with the mailing list as a cc, it is 
not tracked.


3 - when a new question is sent as a reply to an earlier thread with a 
new subject line, it is not tracked. start a new thread for new 
questions with new subject lines.


4 - please use reply-all if you would like more assistance about the 
same subject to keep the thread consistent for the user community.


Thank you for your help with this!

Best,

Jen
Galaxy team


Peng, Tao wrote:

Hi jen, after I did TopHat analysis of groomed FASTAQ data, how can I
find information on how many total reads went into TopHat? How many
reads were removed? How many unique hits to reference genome?

I was trying to prepare a table for presentation and realize that I
could NOT find the information in my GALAXY account?

Thanks,

tao



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[galaxy-user] TopHat/Cufflinks visualization

2011-11-09 Thread Alessia D
How do people on this mailing list usually visualize Tophat and/or
Cufflinks results (eg. tracks on UCSC browser)?

I have only this once before, and I started with a .wig file that I
uploaded to the genome browser, however it looks like Tophat does not give
any .wig file in the output.  Suggestions?

Thanks!

A
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Re: [galaxy-user] TopHat/Cufflinks visualization

2011-11-09 Thread shamsher jagat
Ues IGV  or Galaxy tracker.


On Wed, Nov 9, 2011 at 9:37 AM, Alessia D ad2...@gmail.com wrote:

 How do people on this mailing list usually visualize Tophat and/or
 Cufflinks results (eg. tracks on UCSC browser)?

 I have only this once before, and I started with a .wig file that I
 uploaded to the genome browser, however it looks like Tophat does not give
 any .wig file in the output.  Suggestions?

 Thanks!

 A




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Re: [galaxy-user] TopHat/Cufflinks visualization

2011-11-09 Thread Jennifer Jackson

Hi Alessia,

Shamsher is correct, Trackster is a great choice for viewing data.

The Galaxy Track Browser (aka Trackster) has several new features and 
more coming up in the next few weeks at the Main instance. This tutorial 
covers a basic RNA-seq analysis that includes visualization:

http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise

And this wiki explains the details. One brand new feature (undocumented) 
allows a custom genome to be used in fasta format from your history 
(same basic instructions as in the wiki for a custom genome browser 
creation, but use the fasta file instead of a .len file). So whether 
your genome is native to Galaxy, or UCSC, or not, Trackster can display 
multiple tracks at full chromosome or zoomed view with user-defined 
display options:

http://wiki.g2.bx.psu.edu/Learn/Visualization

Hopefully this will work out for you!

Best,

Jen
Galaxy team

On 11/9/11 9:37 AM, Alessia D wrote:

How do people on this mailing list usually visualize Tophat and/or
Cufflinks results (eg. tracks on UCSC browser)?

I have only this once before, and I started with a .wig file that I
uploaded to the genome browser, however it looks like Tophat does not
give any .wig file in the output.  Suggestions?

Thanks!

A





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Re: [galaxy-user] tophat error

2011-10-12 Thread zohra saci

Thanks Jen for your answer
Zohra

 Date: Tue, 11 Oct 2011 13:01:37 -0400
 From: j...@bx.psu.edu
 To: saci...@live.fr
 CC: galaxy-user@lists.bx.psu.edu
 Subject: Re: [galaxy-user] tophat error
 
 Hi Zohra,
 
 One more bit of help: in the past our team has noticed that Color Space 
 files from NCBI's SRA database have a placeholder adapter base quality 
 score added in (for an unknown reason).
 
 If you choose to use Galaxy, when passing the file through the FASTQ 
 Groomer tool (with input and output type set to cssanger) this extra 
 score is removed. This standardizes the data and makes it useable with 
 analysis tools such as Bowtie/TopHat.
 
 The same thing could be done on the command line (removing the initial 
 qual score for each FASTQ entry) if that is an option for you.
 
 Best wishes for your project,
 
 Jen
 Galaxy team
 
 
 
 
 On 10/11/11 12:14 PM, Jennifer Jackson wrote:
  Hello Zohra,
 
  For command line (not Galaxy) use of this tool, questions would be best
  directed to the tool authors at tophat.cuffli...@gmail.com. That said,
  there appears to be a mismatch between the quality scores in your fastq
  file and what was expected (integer, linked to the -C option).
 
  Should you decide to use Galaxy at http://usegalaxy.org, there are tools
  to format the input and run this type of job. To help you get started,
  please see our tutorial covering this exact type of analysis:
 
  http://wiki.g2.bx.psu.edu/Learn/Screencasts
  see Examples of other analyses - SOLiD Single End
 
  Hopefully one of these options will work out for you,
 
  Best,
 
  Jen
  Galaxy team
 
  On 10/11/11 7:47 AM, zohra saci wrote:
 
 
  Hello,
  I was trying to run tophat v1.3.2 on SOLID data and I have this error:
  *zohra@bart:~/Bureau/cancer$ tophat -o /tmp/tophat_SRR036752/ -g 1 -p 4
  -C /home/zohra/indexes_bowtie/humain_ SRR036752.fastq
 
  [Tue Oct 11 13:23:53 2011] Beginning TopHat run (v1.3.2)
  ---
  [Tue Oct 11 13:23:53 2011] Preparing output location
  /tmp/tophat_SRR036752//
  [Tue Oct 11 13:23:53 2011] Checking for Bowtie index files
  [Tue Oct 11 13:23:53 2011] Checking for reference FASTA file
  [Tue Oct 11 13:23:53 2011] Checking for Bowtie
  Bowtie version: 0.12.7.0
  [Tue Oct 11 13:23:53 2011] Checking for Samtools
  Samtools Version: 0.1.18
  [Tue Oct 11 13:23:53 2011] Generating SAM header for
  /home/zohra/indexes_bowtie/humain_
  [Tue Oct 11 13:23:55 2011] Preparing reads
  format: fastq
  quality scale: phred33 (default)
  [FAILED]
  Error running 'prep_reads'
  Error: qual length (51) differs from seq length (51) for fastq record !
  *
  Can you help me.
  Thanks
  Zohra Saci
 
 
 
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 http://galaxyproject.org/Support
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[galaxy-user] tophat error

2011-10-11 Thread zohra saci






















Hello,
I was trying to run tophat v1.3.2 on SOLID data and I have this error: 
zohra@bart:~/Bureau/cancer$ tophat  -o /tmp/tophat_SRR036752/  -g 1 -p 4 -C 
/home/zohra/indexes_bowtie/humain_ SRR036752.fastq 

[Tue Oct 11 13:23:53 2011] Beginning TopHat run (v1.3.2)
---
[Tue Oct 11 13:23:53 2011] Preparing output location /tmp/tophat_SRR036752//
[Tue Oct 11 13:23:53 2011] Checking for Bowtie index files
[Tue Oct 11 13:23:53 2011] Checking for reference FASTA file
[Tue Oct 11 13:23:53 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Oct 11 13:23:53 2011] Checking for Samtools
Samtools Version: 0.1.18
[Tue Oct 11 13:23:53 2011] Generating SAM header for 
/home/zohra/indexes_bowtie/humain_
[Tue Oct 11 13:23:55 2011] Preparing reads
format: fastq
quality scale: phred33 (default)
[FAILED]
Error running 'prep_reads'
Error: qual length (51) differs from seq length (51) for fastq record !

Can you help me.
Thanks
Zohra Saci





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Re: [galaxy-user] tophat error

2011-10-11 Thread Jennifer Jackson

Hello Zohra,

For command line (not Galaxy) use of this tool, questions would be best 
directed to the tool authors at tophat.cuffli...@gmail.com. That said, 
there appears to be a mismatch between the quality scores in your fastq 
file and what was expected (integer, linked to the -C option).


Should you decide to use Galaxy at http://usegalaxy.org, there are tools 
to format the input and run this type of job. To help you get started, 
please see our tutorial covering this exact type of analysis:


http://wiki.g2.bx.psu.edu/Learn/Screencasts
see Examples of other analyses - SOLiD Single End

Hopefully one of these options will work out for you,

Best,

Jen
Galaxy team

On 10/11/11 7:47 AM, zohra saci wrote:



Hello,
I was trying to run tophat v1.3.2 on SOLID data and I have this error:
*zohra@bart:~/Bureau/cancer$ tophat -o /tmp/tophat_SRR036752/ -g 1 -p 4
-C /home/zohra/indexes_bowtie/humain_ SRR036752.fastq

[Tue Oct 11 13:23:53 2011] Beginning TopHat run (v1.3.2)
---
[Tue Oct 11 13:23:53 2011] Preparing output location /tmp/tophat_SRR036752//
[Tue Oct 11 13:23:53 2011] Checking for Bowtie index files
[Tue Oct 11 13:23:53 2011] Checking for reference FASTA file
[Tue Oct 11 13:23:53 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Oct 11 13:23:53 2011] Checking for Samtools
Samtools Version: 0.1.18
[Tue Oct 11 13:23:53 2011] Generating SAM header for
/home/zohra/indexes_bowtie/humain_
[Tue Oct 11 13:23:55 2011] Preparing reads
format: fastq
quality scale: phred33 (default)
[FAILED]
Error running 'prep_reads'
Error: qual length (51) differs from seq length (51) for fastq record !
*
Can you help me.
Thanks
Zohra Saci



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Re: [galaxy-user] tophat error

2011-10-11 Thread Jennifer Jackson

Hi Zohra,

One more bit of help: in the past our team has noticed that Color Space 
files from NCBI's SRA database have a placeholder adapter base quality 
score added in (for an unknown reason).


If you choose to use Galaxy, when passing the file through the FASTQ 
Groomer tool (with input and output type set to cssanger) this extra 
score is removed. This standardizes the data and makes it useable with 
analysis tools such as Bowtie/TopHat.


The same thing could be done on the command line (removing the initial 
qual score for each FASTQ entry) if that is an option for you.


Best wishes for your project,

Jen
Galaxy team




On 10/11/11 12:14 PM, Jennifer Jackson wrote:

Hello Zohra,

For command line (not Galaxy) use of this tool, questions would be best
directed to the tool authors at tophat.cuffli...@gmail.com. That said,
there appears to be a mismatch between the quality scores in your fastq
file and what was expected (integer, linked to the -C option).

Should you decide to use Galaxy at http://usegalaxy.org, there are tools
to format the input and run this type of job. To help you get started,
please see our tutorial covering this exact type of analysis:

http://wiki.g2.bx.psu.edu/Learn/Screencasts
see Examples of other analyses - SOLiD Single End

Hopefully one of these options will work out for you,

Best,

Jen
Galaxy team

On 10/11/11 7:47 AM, zohra saci wrote:



Hello,
I was trying to run tophat v1.3.2 on SOLID data and I have this error:
*zohra@bart:~/Bureau/cancer$ tophat -o /tmp/tophat_SRR036752/ -g 1 -p 4
-C /home/zohra/indexes_bowtie/humain_ SRR036752.fastq

[Tue Oct 11 13:23:53 2011] Beginning TopHat run (v1.3.2)
---
[Tue Oct 11 13:23:53 2011] Preparing output location
/tmp/tophat_SRR036752//
[Tue Oct 11 13:23:53 2011] Checking for Bowtie index files
[Tue Oct 11 13:23:53 2011] Checking for reference FASTA file
[Tue Oct 11 13:23:53 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Oct 11 13:23:53 2011] Checking for Samtools
Samtools Version: 0.1.18
[Tue Oct 11 13:23:53 2011] Generating SAM header for
/home/zohra/indexes_bowtie/humain_
[Tue Oct 11 13:23:55 2011] Preparing reads
format: fastq
quality scale: phred33 (default)
[FAILED]
Error running 'prep_reads'
Error: qual length (51) differs from seq length (51) for fastq record !
*
Can you help me.
Thanks
Zohra Saci



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Re: [galaxy-user] TopHat--BAM merge

2011-10-03 Thread Jennifer Jackson

Hi Rich,

Are you using a local instance or the main public instance at 
http://usegalaxy.org?


There was a bug fix to this tool on the public instance right around the 
time this error was reported. Please try the job again. If it fails, it 
may be that the files are too large, although an error would be expected.


If after the re-run, the same thing occurs, please share a link to the 
history and we can take a look. Use Options - Share or Publish, 
generate the link, and send directly to me (not the list).


Best,

Jen
Galaxy team

On 9/30/11 9:43 AM, Richard Mark White wrote:

Hi,
I mapped two illumina runs using TopHat (they are from same RNA sample).
Then tried to use the BAM merge tool to make this into one BAM file for
further processes. But it returned an empty file. Is this not possible?
Maybe I am not understanding the purpose/use of BAM merge?

Rich



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[galaxy-user] TopHat--BAM merge

2011-09-30 Thread Richard Mark White
Hi,
  I mapped two illumina runs using TopHat (they are from same RNA sample).  
Then tried to use the BAM merge tool to make this into one BAM file for further 
processes.  But it returned an empty file.  Is this not possible?  Maybe I am 
not understanding the purpose/use of BAM merge?

Rich
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[galaxy-user] TopHat

2011-08-01 Thread Luciano Cosme
Hi,
   I am running galaxy locally and when I perform alignments with TopHat I
get the following error:

Error in tophat:

[Fri Jul 29 17:55:47 2011] Beginning TopHat run (v1.3.1)
---
[Fri Jul 29 17:55:47 2011] Preparing output location ./tophat_out/
[Fri Jul 29 17:55:47 2011] Checking for Bowtie index files
[Fri Jul 29 17:55:47 2011] Checking for reference FASTA file
Warning: Could not find FASTA file /tmp/tmp1dXHLG/dataset_26.dat.fa
[Fri Jul 29 17:55:47 2011] Reconstituting reference FASTA file from Bowtie index
Executing: /bin/bowtie-inspect /tmp/tmp1dXHLG/dataset_26.dat 
./tophat_out/tmp/dataset_26.dat.fa
[Fri Jul 29 17:56:39 2011] Checking for Bowtie
Bowtie version:  0.12.7.0
[Fri Jul 29 17:56:39 2011] Checking for Samtools
Error locating program: samtools

   I installed the samtools (in several places already), but it seems I did
not put it in the right place. So where galaxy search for it?
Thank you.

Luciano
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Re: [galaxy-user] TopHat

2011-08-01 Thread Jennifer Jackson

Hello Luciano,

Here are is the core wiki link to help with NGS tools (including 
SamTools) set up and installation.


http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup

For next time, the galaxy-...@bx.psu.edu mailing list would be the best 
place to send new questions or even follow-up questions to this one if 
problems persist. The development community can be very helpful in 
sorting out local installation issue that may come up. Subscribing may 
also be of interest:

http://lists.bx.psu.edu/listinfo/galaxy-dev
http://galaxyproject.org/Support

Thanks!

Jen
Galaxy team

On 8/1/11 8:53 AM, Luciano Cosme wrote:

Hi,
I am running galaxy locally and when I perform alignments with
TopHat I get the following error:

Error in tophat:

[Fri Jul 29 17:55:47 2011] Beginning TopHat run (v1.3.1)
---
[Fri Jul 29 17:55:47 2011] Preparing output location ./tophat_out/
[Fri Jul 29 17:55:47 2011] Checking for Bowtie index files
[Fri Jul 29 17:55:47 2011] Checking for reference FASTA file
Warning: Could not find FASTA file /tmp/tmp1dXHLG/dataset_26.dat.fa
[Fri Jul 29 17:55:47 2011] Reconstituting reference FASTA file from Bowtie index
Executing: /bin/bowtie-inspect /tmp/tmp1dXHLG/dataset_26.dat  
./tophat_out/tmp/dataset_26.dat.fa
[Fri Jul 29 17:56:39 2011] Checking for Bowtie
Bowtie version:  0.12.7.0
[Fri Jul 29 17:56:39 2011] Checking for Samtools
Error locating program: samtools

I installed the samtools (in several places already), but it seems I
did not put it in the right place. So where galaxy search for it?
Thank you.

Luciano



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Re: [galaxy-user] Tophat error: broken pipe

2011-07-20 Thread Jennifer Jackson

Hi Song,

We have alpha support for Tophat v1.3.0 and it appears to work fine with 
Galaxy's Tophat wrappers. We'll upgrade and start full testing near term.


For now, when running in a local instances, we do encourage users to try 
it and see if it meets their needs. Perhaps try with an uncompressed 
version of the same input file and see if that functions as expected or 
if the same error is given when used with the Galaxy wrappers?


If you want to post testing details (Galaxy pull # from bitbucket, gzip, 
OS version and anything else you feel is relevant) after this sort of 
testing, the development team will use that information when full 
integration testing is performed.


Perhaps others running local instances will also comment if you post 
these detailed testing results to the galaxy-...@bx.psu.edu mailing list 
(will reach the primary external Galaxy development community).


Thanks for using Galaxy!

Jen
Galaxy team

On 7/20/11 6:59 AM, Song Li wrote:


Hi Jen,

Thank you for the fast reply, however, tophat works fine with this
command when used as stand alone software. I checked the version of gzip
and it's the same on galaxy server and on the machine where I run tophat
alone.

The broken pipe error is likely due to a file that is not closed by a
previous step.

Have anyone tested tophat 1.3 on galaxy?

Thanks,
Song

On Tue 07/19/11 6:45 PM , Jennifer Jackson j...@bx.psu.edu wrote:

Hello Song Li,

The file extension seems to be a mismatch.

file.gz - gzip utility

Exploring the use of gunzip or zcat are options to restore a file.z.

Hopefully this helps,

Jen
Galaxy team

On 7/19/11 11:52 AM, Song Li wrote:
  Hello everyone,

  I was trying to run tophat in a local version of galaxy, but I got the
  following error:

  gzip: stdout: Broken pipe
  [Tue Jul 19 14:10:36 2011] Processing bowtie hits
  Error: could not open pipe gzip -cd
./tophat_out/tmp/left_kept_reads_missing.fq.z

  It seems that when tophat is calling gzip, the pipe can not be open.

  Can anyone suggest a fix to this problem?

  Thanks,
  Song Li
  --
  Postdoctoral Associate
  Uwe Ohler Laboratory
  Institute for Genome Sciences and Policy
  101 Science Drive
  CIEMAS 2171
  Phone: 919-68-2124
  Duke University



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[galaxy-user] Tophat error: broken pipe

2011-07-19 Thread Song Li
Hello everyone,

I was trying to run tophat in a local version of galaxy, but I got the
following error:

gzip: stdout: Broken pipe
[Tue Jul 19 14:10:36 2011] Processing bowtie hits
Error: could not open pipe gzip -cd 
./tophat_out/tmp/left_kept_reads_missing.fq.z

It seems that when tophat is calling gzip, the pipe can not be open.

Can anyone suggest a fix to this problem?

Thanks,
Song Li
-- 
Postdoctoral Associate
Uwe Ohler Laboratory
Institute for Genome Sciences and Policy
101 Science Drive
CIEMAS 2171
Phone: 919-68-2124
Duke University
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Re: [galaxy-user] Tophat error: broken pipe

2011-07-19 Thread Jennifer Jackson

Hello Song Li,

The file extension seems to be a mismatch.

file.gz - gzip utility

Exploring the use of gunzip or zcat are options to restore a file.z.

Hopefully this helps,

Jen
Galaxy team

On 7/19/11 11:52 AM, Song Li wrote:

Hello everyone,

I was trying to run tophat in a local version of galaxy, but I got the
following error:

gzip: stdout: Broken pipe
[Tue Jul 19 14:10:36 2011] Processing bowtie hits
Error: could not open pipe gzip -cd  
./tophat_out/tmp/left_kept_reads_missing.fq.z

It seems that when tophat is calling gzip, the pipe can not be open.

Can anyone suggest a fix to this problem?

Thanks,
Song Li
--
Postdoctoral Associate
Uwe Ohler Laboratory
Institute for Genome Sciences and Policy
101 Science Drive
CIEMAS 2171
Phone: 919-68-2124
Duke University



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[galaxy-user] Tophat error

2011-06-29 Thread Simon Lank
Hi. Newbie here. I'm trying to setup tophat for our local install. I'm
getting the following error when I try to run it. Has anyone seen this
before or have any ideas what I can try to fix it.

Thanks,

Simon

Error in tophat:

[Wed Jun 29 11:54:09 2011] Beginning TopHat run (v1.3.1)
---
[Wed Jun 29 11:54:09 2011] Preparing output location ./tophat_out/
[Wed Jun 29 11:54:09 2011] Checking for Bowtie index files
[Wed Jun 29 11:54:09 2011] Checking for reference FASTA file
Warning: Could not find FASTA file
/var/folders/f1/f1aTv8DnERiCv5ic7O3rlk++-+6/-Tmp-/tmpe7Oa0l/dataset_127234.dat.fa
[Wed Jun 29 11:54:09 2011] Reconstituting reference FASTA file from Bowtie index
Executing: /Volumes/storagepool/oconnorlab/galaxy_dist/bin/bowtie-inspect
/var/folders/f1/f1aTv8DnERiCv5ic7O3rlk++-+6/-Tmp-/tmpe7Oa0l/dataset_127234.dat
 ./tophat_out/tmp/dataset_127234.dat.fa
[Wed Jun 29 11:54:09 2011] Checking for Bowtie
Bowtie version:  0.12.5.0
[Wed Jun 29 11:54:09 2011] Checking for Samtools
Samtools Version: 0.1.7
[Wed Jun 29 11:54:09 2011] Generating SAM header for
/var/folders/f1/f1aTv8DnERiCv5ic7O3rlk++-+6/-Tmp-/tmpe7Oa0l/dataset_127234.dat
[Wed Jun 29 11:54:09 2011] Preparing reads
format:  fastq
quality scale:   phred33 (default)
Left  reads: min. length=17, count=2666051
Warning: short reads (20bp) will make TopHat quite slow and take
large amount of memory because they are likely to be mapped to too
many places
[Wed Jun 29 11:54:27 2011] Mapping left_kept_reads against
dataset_127234.dat with Bowtie

gzip: stdout: Broken pipe
[Wed Jun 29 11:54:27 2011] Processing bowtie hits
Traceback (most recent call last):
  File /Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat, line 2607, in
sys.exit(main())
  File /Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat, line
2566, in main
user_supplied_deletions)
  File /Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat, line
2256, in spliced_alignment
ref_fasta)
  File /Volumes/storagepool/oconnorlab/galaxy_dist/bin/tophat, line
2000, in junctions_from_segments
if left_reads_map != left_seg_maps[0]:
IndexError: list index out of range
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Re: [galaxy-user] Tophat version

2011-03-23 Thread Jennifer Jackson

Hi David,

Will be updated to 1.2.0 when main is next updated (soon).

Once implemented, feedback about how the update functions would be welcomed,

Best,
Jen

On 3/14/11 1:14 PM, David Matthews wrote:

Hi,

Just wondering when the tophat portion of Galaxy will be updated? Its currently 
version 1.1.1 and there is now a version 1.2.0 (in fact I think there have been 
4 updates).

Cheers
David


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[galaxy-user] Tophat version

2011-03-14 Thread David Matthews
Hi,

Just wondering when the tophat portion of Galaxy will be updated? Its currently 
version 1.1.1 and there is now a version 1.2.0 (in fact I think there have been 
4 updates).

Cheers
David


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