Thread: cuffmerge error
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Old 05-30-2012, 07:56 AM   #1
wangli
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Location: Texas

Join Date: Apr 2012
Posts: 48
Default cuffmerge error

Hi, I am confronted with some errors when doing cuffmerge analysis.

/home/bin/cuffmerge -g Ptrichocarpa_156_gene.gff3 -s Ptrichocarpa_156_hardmasked.fa -p 10 assemblies.txt

[Wed May 30 09:48:20 2012] Converting GTF files to SAM
[FAILED]
Error: gtf_to_sam not found on this system. Did you forget to include it in your PATH?

I checked very carefully with my directory /home/bin and found that gtf_to_sam is actually in this directory. I cannot understand why the software cannot find it.

Sorry for my naive questions.

Any comments are very appreciated.
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