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Cuffmerge error : cuffcompare not found

I already done running cufflink, then I used cuffmerge and execute the following command :

 /home/crystalum/cufflinks-2.2.1.Linux_x86_64/cuffmerge -o newmergedfile -g /home/crystalum/MATINE/index/gencode.v21.annotation.gtf -s /home/crystalum/MATINE/index/Hg38.fa -p 19 finalassamblies.txt

But I am getting following error:

**(Comparing against reference file /home/crystalum/MATINE/index/gencode.v21.annotation.gtf
/bin/sh: 1: cuffcompare: not found
    [FAILED]
Error: could not execute cuffcompare)**

I guess the problem is PATH , but I already change the path to the cuffcompre in cuffmerge file , but still the error appears .

Thank you for your help, Matine

assembly
• 2,198 views • link
updated by collinsagho • collinsagho • written by matine • matine

change the path to the cuffcompre in cuffmerge file

Did you mean to say cuffmerge folder?

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written by GenoMax GenoMax

Thank you for your replay, I already fixed the problem. just changed the path to Cuffcompare in the Cuffmerge file

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written by matine • matine

How did you change the PATH? The exact command?

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written by h.mon h.mon

I just copy paste the path of Cuffcompare into Cuffmerge script

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written by matine • matine

1 answer

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written by collinsagho • collinsagho

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