How Does Cuffdiff Identify The Bam File To Corresponding Condition Before Performing The De Analysis?

Question

[k.nirmalraman]

Where in cuffdiff we can specify that the bam files are associated to different conditions?

cuffdiff -o outputname -b genome.fasta -p <cores>  -L C1, C2 -u merged.gtf C1R1/accepted_hits.bam C2R1/accepted_hits.bam C1R1/accepted_hits.bam C2R2/accepted_hits.bam

How does this association work? does option L needs to be specified like C1,C2,C1,C2.

Any help would be greatly appreciated.

Answer 1

[Devon Ryan]

You need something of the form:

cuffdiff -o outputname -b genome.fasta -p <cores> -L C1,C2 -u merged.gtf C1R1/accepted_hits.bam,C1R2/accepted_hits.bam C2R1/accepted_hits.bam,C2R2/accepted_hits.bam

Note the lack of spaces following the commas. Group members should be separated by commas with no spaces (with a space between the groups). The label is then applied in the order that the groups are input.

[k.nirmalraman]

Thank you.. My bad.. missed the space part!!