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Question: RNA-Seq Alignment too Big for Galaxy?
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gravatar for Newbie
11 months ago by
Newbie • 0
Newbie • 0 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.

hisat star rna-seq rnastar hisat2 • 371 views
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modified 11 months ago by Jennifer Hillman Jackson ♦ 25k • written 11 months ago by Newbie • 0
1

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

ADD REPLY • link written 11 months ago by Devon Ryan • 1.9k
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gravatar for Jennifer Hillman Jackson
11 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 11 months ago by Jennifer Hillman Jackson ♦ 25k
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