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Old 05-05-2015, 01:00 AM   #1
bvk
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Default Error While Running Cuffdiff for Groups

I'm trying to run cuffdiff for two groups. each has one sample for example I gave the following command:

cuffdiff -o diff_out3 -b ../genome/ce7.fa -p 2 -L em,la -u ../cufflinks/merged_asm/merged.gtf em/SRR493423_thout/accepted_hits.bam la/SRR872399_thout/accepted_hits.bam

Last edited by bvk; 05-06-2015 at 03:05 AM.
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Old 05-05-2015, 01:09 AM   #2
GenoMax
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This may sound odd but can you try replacing "em" and "la" with something else (longer names)?
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Old 05-05-2015, 01:17 AM   #3
bvk
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Quote:
Originally Posted by GenoMax View Post
This may sound odd but can you try replacing "em" and "la" with something else (longer names)?
nope that's not the problem
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