Question: RNA-Seq Alignment too Big for Galaxy?
0
gravatar for Newbie
6 weeks ago by
Newbie0
Newbie0 wrote:

Hello,

I have relatively large trimmed FASTQsanger files that I want to align via Star and eventually do differential expression analysis on. However, I keep getting the error "Remote job server indicated a problem running or monitoring this job.". The FASTQsanger files are paired-end and the following sizes (R2 of the samples being the same size):

1-R1 (12.5 GB)

2-R1 (21.1 GB)

3-R1 (29.5 GB)

4-R1 (15.0 GB)

Are these files too large for the server to process correctly? If so, should I separate them into smaller files and then combine the mapped Star bam file? How would I do that exactly? Thank you.

ADD COMMENTlink modified 5 weeks ago by Jennifer Hillman Jackson23k • written 6 weeks ago by Newbie0
1

Those aren't too big. Are you running this on usegalaxy.org or a different Galaxy server?

ADD REPLYlink written 5 weeks ago by Devon Ryan1.9k
0
gravatar for Jennifer Hillman Jackson
5 weeks ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

HISAT2 is recommended over RNA STAR when working at https://usegalaxy.org. STAR uses much more resource to map the same data.

If you cannot determine the problem and/or HISAT2 also fails, a bug report can be sent in from one of the failed jobs.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 5 weeks ago by Jennifer Hillman Jackson23k
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