Question: TopHat not processing RNA-seq FASTQ file
2
gravatar for ang3x
22 months ago by
ang3x20
ang3x20 wrote:

Usually have no problem with TopHat processing of RNA-seq FASTQ files. Currently using a file that is a little larger (16 gb) than previous (4-5 gb). When file is submitted, it is stuck in queue really long and then the resultant TopHat files are all empty.

rna-seq • 507 views
ADD COMMENTlink modified 22 months ago by Jennifer Hillman Jackson24k • written 22 months ago by ang3x20
1

Hello All,

Been having exactly the same issue since Friday morning (UK - GMT Time). Run TopHat as a control on fastq files that I know worked fine when loaded previously into tophat and this time everything came up blank.

ADD REPLYlink written 22 months ago by VY120
1

Hello,

Would one of you please share a history demonstrating the problem. A small history is best. Start by copying the datasets related to the problem into a new history. Include all datasets in the analysis thread leading up to and including the Tophat problem (the fastq data uploaded, all intermediate manipulations the tophat runs). If a custom genome was used, copy that as well. Make sure all datasets are active (not hidden/deleted/perm deleted).

How to copy: https://wiki.galaxyproject.org/Learn/ManagingDatasets#Copy How to share: https://wiki.galaxyproject.org/Learn/Share

Send an email to galaxy-bugs@lists.galaxyproject.org from the same email that you use for your account at http://usegalaxy.org, note your user name here, and include a link to this post. I will also test independently.

More that one person can share a history - a few examples could help.

Thanks, Jen, Galaxy team

ADD REPLYlink written 22 months ago by Jennifer Hillman Jackson24k
1

Hi Galaxy team,

Thanks for the quick reply. Here is the representative history for the reported issue: https://usegalaxy.org/u/apen/h/tophatbug The same issue has also been reported to galaxy-bugs@lists.galaxyproject.org

Thanks again,

ADD REPLYlink written 22 months ago by apengood20
1

Hi Galaxy team,

I have experiencing the same problem but getting the following message with my empty bam files:

Log: tool progress Log: tool progress /galaxy-repl/main/jobdir/013/266/13266476/tool_script.sh: line 9: tophat2: command not found

I have also noticed that the old versions of tophat work on my data so I guess it is a problem with the new update (2.1)

ADD REPLYlink written 22 months ago by matthew.ford10

Hi Galaxy team,

I experienced the same problem as the issue posted by and3x. The TopHat that map the fastq data to the reference genome generated empty outputs. No error message was shown from the outputs.

ADD REPLYlink written 22 months ago by apengood20

Hi Galaxy team,

I experienced the same problem as the issue posted by and3x. The TopHat that map the fastq data to the reference genome generated empty outputs. No error message was shown from the outputs.

ADD REPLYlink written 22 months ago by apengood20
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 96 users visited in the last hour