Question: Error While Running Cuffdiff On Multiple Bam Files Of A Group
0
gravatar for Jordan
6.3 years ago by
Jordan1.1k
Pittsburgh
Jordan1.1k wrote:

Hi,

I'm trying to run cuffdiff on 6 samples, divided into two groups of 3 samples each - G1(Female), G2(Male). But, it does not run. I gave the following command:

cuffdiff /refs/mm9/Annotation/Genes/genes.gtf -L G1,G2 ~/Female/sampleA/accepted_hits.bam,~/Female/sampleC/accepted_hits.bam,~/Female/sampleE/accepted_hits.bam ~/Male/sampleG/accepted_hits.bam,~/Male/sampleI/accepted_hits.bam,~/Male/sampleK/accepted_hits.bam

I get this error:

You are using Cufflinks v2.1.1, which is the most recent release.
open: No such file or directory
File ~/Female/sampleC/accepted_hits.bam doesn't appear to be a valid BAM file, trying SAM...
Error: cannot open alignment file ~/Female/sampleC/accepted_hits.bam for reading

I have generated these BAM files using tophat2. They are mouse genome. But they seem to work when I give single bam file of the same group. Like the following command.

cuffdiff /refs/mm9/Annotation/Genes/genes.gtf -L G1,G2 ~/Female/sampleA/accepted_hits.bam ~/Male/sampleG/accepted_hits.bam

Can anyone tell me how to run multiple bam files of a group on cuffdiff?

tophat2 cuffdiff rna-seq • 5.1k views
ADD COMMENTlink modified 6.3 years ago by Pierre Lindenbaum126k • written 6.3 years ago by Jordan1.1k
0
gravatar for Pierre Lindenbaum
6.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum126k wrote:

replace '~' by ${HOME}.

$ echo A,~/B
A,~/B

$ echo A,${HOME}/B
A,/home/lindenb/B
ADD COMMENTlink modified 6.3 years ago • written 6.3 years ago by Pierre Lindenbaum126k

That worked. Thanks! But out of curiosity, can you explain why that works?

ADD REPLYlink written 6.3 years ago by Jordan1.1k
1

see http://www.gnu.org/software/bash/manual/html_node/Tilde-Expansion.html ",~" is not the beginning of a word.

ADD REPLYlink written 6.3 years ago by Pierre Lindenbaum126k

That helped. Thanks again!

ADD REPLYlink written 6.3 years ago by Jordan1.1k
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