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  • Cufflinks - 'u' Class Code - Consistently Returned

    Steps taken:

    KEY:
    MCF_7_cDNA_fragments.sam (2X100 cDNA paired end aligned reads from MCF-7 cell line)

    1. cufflinks -m 400 -p 10 -L MCF_7_transcript MCF_7_cDNA_fragments.sam

    KEY:
    transcripts.gtf (transcripts assembled from step 1)
    Homo_sapiens.GRCh37.58.gtf ("reference" annotation from Ensembl)

    2. cuffcompare -r Homo_sapiens.GRCh37.58.gtf transcripts.gtf

    PROBLEM: The .tmap file lists all assembled transcripts as 'unknown intergenic transcripts' (class code "u")

    Would this make sense if there wasn't any MCF-7 transcripts in the supplied reference file? Or how could this be?

    Thanks for any help you can offer.
    Last edited by AndrewCarpenter; 07-19-2010, 07:04 AM. Reason: Wasn't explicit enough.

  • #2
    Cuffcompare Output Seems Incorrect

    Steps taken:

    KEY:
    MCF_7_cDNA_fragments.sam (2X100 cDNA paired end aligned reads from MCF-7 cell line)

    Code:
    1. cufflinks -m 400 -p 10 -L MCF_7_transcript MCF_7_cDNA_fragments.sam
    KEY:
    transcripts.gtf (transcripts assembled from step 1)
    Homo_sapiens.GRCh37.58.gtf ("reference" annotation from Ensembl)

    Code:
    2. cuffcompare -r Homo_sapiens.GRCh37.58.gtf transcripts.gtf
    PROBLEM: The .tmap file lists all assembled transcripts as 'unknown intergenic transcripts' (class code "u")

    Would this make sense if there wasn't any MCF-7 transcripts in the supplied reference file? Or how could this be?

    Thanks for any help you can offer.

    Comment


    • #3
      Hi there.

      I have the same problem with the latest version of Human Ensembl reference file.
      (Homo_sapiens.GRCh37.60.gtf). I have added 'chr' in front of each chromosome number (beginning of each line) - as this was required when I did previous Cufflinks analysis with Homo_sapiens.GRCh37.55.gtf.

      Cufflinks analysis worked well with the v55 of the reference file, but only see 'u' matches with the .60 version of the file. The only formatting difference I see between the two files is spaces between fields instead of tabs as in the v55 file. I have tried editing the file so the v60 file has tabs too - but this didn't help, in fact Cufflinks couldn't read the reference file.

      Have you managed to solve your problem?

      Cheers

      Comment


      • #4
        the difference between reference and gtf file

        Hi,everyone

        I had the same probrem that the cuffcompare output .tmap file had only 'u'.

        I just resolved this to make chromosome names between reference.gtf and my gtf file from cufflinks equal.

        I hope this will help you

        Comment

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