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
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?