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Old 08-18-2014, 07:45 AM   #1
thickrick99
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Location: Washington

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Question Cuffmerge can't execute gtf_to_sam

Hi Everyone,

I am having some issues with cuff merge right now because it is giving me an error that it could not execute gtf_to_sam. I have seen other questions posted about this but couldn't find a solution that worked for me. I am using cufflinks version 2.1.1 and here is the command I used:

Code:
cuffmerge -g Homo_sapiens.knownGene.hg19.sorted.withGenes.gtf -s hg19.fa -p 2 assemblies.txt
I tried to run gtf_to_sam separately and it gave me a segmentation fault: 11 error. I am not sure if this is a regular error in cuffmerge or if there is something wrong with the program. I am thinking it may be a problem with my GTF file but I am not sure.

Thanks in advance!!

Last edited by thickrick99; 08-18-2014 at 07:48 AM.
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Old 08-18-2014, 11:34 AM   #2
thickrick99
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I also tried this with a newer version of cufflinks and it did not work.. still giving me the same error.
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