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  • Cuffcopmare: errors when using UCSC known genes

    Hi all,
    I am trying to use cuffcompare (v0.9.2Beta) to compare my rebuilt transcriptome with UCSC known gene annotations. However, I got the error messages though I did obtain the combined.gtf and .tracking files eventually. Any explainations?
    Thank you.

    GFF Warning: discarded overlapping feature segment (40547903-40548425) for GFF ID uc007aug.1
    .....
    Warning: transcript uc008hap.1 discarded (structural errors found, length=261032).

    Warning: found 10930 transcripts with undetermined strand.
    Warning: found 139706 transcripts with undetermined strand.

  • #2
    One of your annotation files is not correct in the placement of strand information. I would start there.

    Comment


    • #3
      Hi RockChalkJayhawk, thanks for your reply. Unfortunately, I do not quite understand what you are saying. Could you say more about that? The annotation I used was the standard GTF file of UCSC known genes. Thanks again.

      Comment


      • #4
        Use one of these GTFs and see if your problem is solved. But first you will need to modify it
        Code:
        awk '{print"chr"$0}' Ensemble.GTF > New.gtf

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        • #5
          I tried to use Ensemble annotation as reference and it does not have problem. However, I would like to use UCSC KNOWN GENES as reference. Did you have the same warning messages when you use known gene annotations? Thank you.

          Comment


          • #6
            Part of the problem is because the gene_id and transcript_id are all the same when you try to export from UCSC. Is there a reason you don't want to use the ENSEMBLE?

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            • #7
              I see.
              In my mind, UCSC known genes include more annotations than Ensemble. I just want to make sure that the "new isoforms" reconstructed is truly new.

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