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  • jay2008
    Member
    • Sep 2010
    • 44
    #1

    is it bug in cufflinks?

    hello,
    I run cufflinks and got the following transcripts from transcript.gtf:
    chrX Cufflinks transcript 107821319 107840299 1000 + . gene_id "CUFF.33619";transcript_id "CUFF.33619.1"; FPKM "9.8800098066"
    ...
    chrX Cufflinks transcript 107840614 107940873 1000 +chrX Cufflinks transcript 107683040 107816842...
    ...
    chrX Cufflinks transcript 107821319 107840299 1000 + . gene_id "CUFF.33619"; transcript_id "CUFF.33619.1"; FPKM "9.8193962495"

    I have several problems:
    (1) the middle of the second "1000+chrX", what does it means?
    (2) the first and third rows share the same transcript id "CUFF.33619.1". what is the reason to repeat the same transcript?
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