How Does Cuffdiff Identify The Bam File To Corresponding Condition Before Performing The De Analysis?
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9.8 years ago
k.nirmalraman ★ 1.1k

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.

cuffdiff • 2.6k views
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Entering edit mode
9.8 years ago

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.

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

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