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 aft
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 thi
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 hum
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
G
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(Can
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 f
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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The Galaxy User list should be
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 t
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
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
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)
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 distri
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
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 her
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 mov
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
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
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 Toxico
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 tr
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-g
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 s
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 Str
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
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.
--
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.
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
_
Hello Xiefan,
On 9/10/12 12:16 PM, Xiefan Fang wrote:
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 thes
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. E
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 n
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
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
___
The Galaxy User
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 "TopH
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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The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public se
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 discuss
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
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
Hi Jiwen,
Please submit this error using the green bug icon associated with the dataset
and we can check to see if this is related to the other issues discussed
earlier today.
Thank you,
Jen
Galaxy Team
On Apr 27, 2012, at 3:18 PM, 杨继文 wrote:
> Hi all,
> I got the following error infomation
Hi all,
I got the following error infomation during Tophat mapping
An error occurred running this job: Job output not returned by PBS: the output
datasets were deleted while the job was running, the job was manually dequeued
or there was a cluster error.
Please let me know what's wrong.
Help
> 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.
Bes
On Wed, Apr 18, 2012 at 8:37 AM, Jeremy Goecks 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
> 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 pos
Hi,
After mapping RNA-Seq paired end reads with Tophat, I can see that most of
reads fall into the right regions. However, I still can see lots of reads
mapped to non-coding region (the locations where the reads are mapped to don't
contain exons).
I am wondering if these "non-coding reads"
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 agai
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 i
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
___
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 ques
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
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
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
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
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
whe
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
:-
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_
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
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
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
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.
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 T
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, howev
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.
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-se
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 calc
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 th
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.
-
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 ma
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://mai
Ues IGV or Galaxy tracker.
On Wed, Nov 9, 2011 at 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 br
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. Suggestion
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 notice
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
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).
S
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)
---
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
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
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 questio
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
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 uncompre
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
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 cal
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)
--
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
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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