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  • CuffLinks / CuffDiff GTF Compatibility

    Hi,

    I want to use CuffDiff to call DE between two samples that I've aligned with TopHat.

    Rather than creating a GTF via CuffLinks, I used one from UCSC (RefSeq). Since the manual suggests the GTF can be from sources other than CuffLinks, I assume this isn't a problem?

    One thing that confuses me, however, is that CuffLinks seems to creating 0-based coordinates in its GTF (as per manual), while the GTF 2.2 standard calls for 1-based coordinates.

    Since the UCSC GTF uses 1-based, does that mean UCSC GTF files are incompatible with CuffDiff?

    Thanks,
    Bio
    Last edited by Bio.X2Y; 06-07-2010, 11:26 AM. Reason: Got my 0s and 1s mixed up...

  • #2
    I've raised this question on the Bowtie sourceforge (I can't find a place to raise CuffLinks specific questions/bugs):


    Text:
    Am I correct in thinking that the CuffLinks GTF files are non-standard? They use 0-based coordinates as per the manual, while GTF2.2 requires 1-based. Does this mean that CuffDiff is not compatible with UCSC or Ensembl GTFs?

    Comment


    • #3
      While describing the start column of the transcripts.gtf file, cufflinks manual (http://cufflinks.cbcb.umd.edu/manual...fflinks_output) states:

      The leftmost coordinate of this record (where 1 is the leftmost possible coordinate)
      Therefore, it should be 1-based.
      Last edited by Marcelo_Alejandro; 08-17-2011, 11:55 AM.

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