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  • hsmart
    Member
    • Dec 2009
    • 15
    #1

    Cufflinks

    Hi All,

    I am trying use Cufflinks with output of tophat. The command is as follow:

    cufflinks HTERT_tophat_accepted_hits.sam.sorted -G Homo_sapiens.GRCh37.56.gtf -L HTERT

    However, Cufflinks just stops after processing bundle for all chromosomes for example,
    Processing bundle [ chrY:59362092-59362127 ] with 1 non-redundant alignments

    There are no data in output files. Can anyone please help me with it?

    Thanks,

    Rakesh
    Tags: None
    • Thomas Doktor
      Senior Member
      • Apr 2009
      • 105
      #2
      I think the likely explanation is that your reference GTF file needs to be reformated.

      You should check out this thread: http://seqanswers.com/forums/showthread.php?t=3972

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