Can Cufflink calculate several biological replicates one time?

[EricHole]

Hi ALL,
I have 8 biological replicates and I do not want to calculate them one by one. What should I do ? May I use Cuffdiff to achieve this goal?
Best!

[mknut]

You can pool together your replicates by submitting them as comma-separated list of files when running cuffdiff. For example:

cuffdiff -o out transcripts.gtf cond1rep1.bam,cond1rep2.bam,cond1rep3.bam cond2rep1.bam,cond2rep2.bam,cond2rep3.bam

note that comma separates replicates within one condition and space separates conditions. It is all in the manual http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff

[EricHole]

You can pool together your replicates by submitting them as comma-separated list of files when running cuffdiff. For example:

cuffdiff -o out transcripts.gtf cond1rep1.bam,cond1rep2.bam,cond1rep3.bam cond2rep1.bam,cond2rep2.bam,cond2rep3.bam

note that comma separates replicates within one condition and space separates conditions. It is all in the manual http://cufflinks.cbcb.umd.edu/manual.html#cuffdiff

Thank you for your reply. I just feel it is very strange that cufflink can't deal with replicates in one time.