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  • Filtering "merge.gtf" (from cuffmerge) by redundance

    I am trying to filter my merge.gtf file produced by ~100 samples by redundancy, I would like to remove the transcripts/isoforms that occur in only one sample. But I didnt find a way to track this information (where each transcript come from) easily!

    Thanks a lot!

  • #2
    Ok, I solved my problem just by using cuffcompare instead of cuffmerge.

    Comment


    • #3
      Here's another thread on this topic of whether to use cuffmerge or cuffcompare. Cole Trapnell and the cufflinks team is soon releasing a protocol paper that will hopefully address some of these issues.

      You might think twice about using cuffcompare over cuffmerge.
      Last edited by turnersd; 02-13-2012, 05:42 AM. Reason: cuffmerge vs cuffcompare

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      • #4
        Thank you turnersd, actually I am using the second approach described on that thread "assemble each bam and cuffcompare them to get a combined.gtf".

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