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  • Can Cufflink calculate several biological replicates one time?

    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!

  • #2
    You can pool together your replicates by submitting them as comma-separated list of files when running cuffdiff. For example:
    Code:
    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

    Comment


    • #3
      Originally posted by mknut View Post
      You can pool together your replicates by submitting them as comma-separated list of files when running cuffdiff. For example:
      Code:
      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.

      Comment

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