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

[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

[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

[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

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-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. ___ The Galaxy User list should be

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

[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

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

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

[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)

[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

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

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

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

[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?

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

[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

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

[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

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

[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

[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. --

Re: [galaxy-user] Tophat alignment statistics?

2012-12-06 Thread Praveen Raj Somarajan
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

[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

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.

[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

[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

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.

[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 ___ The Galaxy User

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

[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 ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public

[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

[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

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

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

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

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,

[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

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

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

[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

[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

[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

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

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

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

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

[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.

[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

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

[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

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

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

[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.

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,

[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

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

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

[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.

[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

[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.

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

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:

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

[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)

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).

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

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

[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

[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/

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

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

[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

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-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)

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

[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 ___ The Galaxy User list should be used for the