Question: How Does Cuffdiff Identify The Bam File To Corresponding Condition Before Performing The De Analysis?
gravatar for k.nirmalraman
5.4 years ago by
k.nirmalraman980 wrote:

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 • 1.8k views
ADD COMMENTlink modified 4.2 years ago by Biostar ♦♦ 20 • written 5.4 years ago by k.nirmalraman980
gravatar for Devon Ryan
5.4 years ago by
Devon Ryan89k
Freiburg, Germany
Devon Ryan89k wrote:

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.

ADD COMMENTlink written 5.4 years ago by Devon Ryan89k

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

ADD REPLYlink written 5.4 years ago by k.nirmalraman980
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