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  • papori
    Senior Member
    • Dec 2010
    • 181
    #1

    length of transcript in cufflinks output

    Hi, how can i know the length of a transcript in gtf format?
    for example if i have this output:

    chr1 Cufflinks transcript 2390 5119 648 + . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; FPKM "0.2916746997"; frac "0.701528"; conf_lo "0.000000"; conf_hi "1.371813"; cov "1.476969";
    chr1 Cufflinks exon 2390 3930 648 + . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "1"; FPKM "0.2916746997"; frac "0.701528"; conf_lo "0.000000"; conf_hi "1.371813"; cov "1.476969";
    chr1 Cufflinks exon 4646 5119 648 + . gene_id "CUFF.7"; transcript_id "CUFF.7.1"; exon_number "2"; FPKM "0.2916746997"; frac "0.701528"; conf_lo "0.000000"; conf_hi "1.371813"; cov "1.476969";
    chr1 Cufflinks transcript 4538 5119 1000 + . gene_id "CUFF.7"; transcript_id "CUFF.7.2"; FPKM "0.4497906122"; frac "0.298472"; conf_lo "0.000000"; conf_hi "1.791119"; cov "2.277629";
    chr1 Cufflinks exon 4538 5119 1000 + . gene_id "CUFF.7"; transcript_id "CUFF.7.2"; exon_number "1"; FPKM "0.4497906122"; frac "0.298472"; conf_lo "0.000000"; conf_hi "1.791119"; cov "2.277629";
    chr1 Cufflinks transcript 5740 6381 1000 . . gene_id "CUFF.13"; transcript_id "CUFF.13.1"; FPKM "0.3842751284"; frac "1.000000"; conf_lo "0.000000"; conf_hi "1.624074"; cov "2.445545";
    chr1 Cufflinks exon 5740 6381 1000 . . gene_id "CUFF.13"; transcript_id "CUFF.13.1"; exon_number "1"; FPKM "0.3842751284"; frac "1.000000"; conf_lo "0.000000"; conf_hi "1.624074"; cov "2.445545";
    c


    thanks!
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