Odd Bug?: No transcripts.gtf from Cufflink output
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6.9 years ago
ntjxv7 ▴ 10

So I think I have found an odd bug for cufflinks, that I can not find any mention of it in any blogs online.  

Bug Explanation:

For output while running cufflinks, sometimes I received a "transcripts.gtf" file and sometimes I do not.  Same gtf input files and options for cufflinks are used.  I have repeated it twice now with the same results.  The only difference is a different bam file.

Cufflinks Input: 

cufflinks -p [number of threads to use] -g [path to Rat gtf file] -o [path for output directory] [.bam file]

For background:

Performing RNA-Seq analysis on several hundred rat samples in order to provide an expression profile.  I have run tophat 2.0 to align fasta files to the current rat genome to generate the .bam files.  Using cufflinks 2.2 to generate the transcripts.gtf in order to make a new gtf reference file to merge downstream with cuffmerge in order to perform cuffdiff analysis.  This protocol has been recommended by trapnell et al and I have successfully run the protocol using human, rat (different), mouse, and dog data.  This is the first time I have come across this problem.  

Any suggestions or possible solutions?

RNA-Seq Cufflinks • 2.4k views
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Entering edit mode
6.9 years ago
ntjxv7 ▴ 10

For those that have run into this problem, its a thread problem.  

The number of threads called from the machine did not match the number of threads cufflinks used.

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> The number of threads called from the machine did not match the number of threads cufflinks used.

How does that happen?

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Entering edit mode
6.9 years ago
ntjxv7 ▴ 10

I'm not sure if this is the case for any other locations, but at least at my location we have community-wide used servers where we use a que to request the number of threads and memory our program will need to run.  There was a mismatch in the number of threads requested and the number cufflinks was using, which created this odd bug.  

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