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  • ECHo
    Member
    • Jan 2010
    • 17

    #1

    Cufflinks GTF file

    The following is excepted from my gtf file, which is produced by Cufflinks:

    chr21 Cufflinks transcript 14304464 14305055 1000 + . gene_id "CUFF.299"; transcript_id "CUFF.299.0"; RPKM "2357.2184844433"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "19.187970";
    chr21 Cufflinks exon 14304464 14304509 1000 + . gene_id "CUFF.299"; transcript_id "CUFF.299.0"; exon_number "1"; RPKM "2357.2184844433"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "19.187970";
    chr21 Cufflinks exon 14304969 14305055 1000 + . gene_id "CUFF.299"; transcript_id "CUFF.299.0"; exon_number "2"; RPKM "2357.2184844433"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "19.187970";
    chr21 Cufflinks transcript 14305973 14306356 1000 + . gene_id "CUFF.302"; transcript_id "CUFF.302.0"; RPKM "491.3950759106"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "4.000000";
    chr21 Cufflinks exon 14305973 14306002 1000 + . gene_id "CUFF.302"; transcript_id "CUFF.302.0"; exon_number "1"; RPKM "491.3950759106"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "4.000000";
    chr21 Cufflinks exon 14306312 14306356 1000 + . gene_id "CUFF.302"; transcript_id "CUFF.302.0"; exon_number "2"; RPKM "491.3950759106"; frac "1.000000"; conf_lo "0.000000"; conf_hi "0.000000"; cov "4.000000";

    The "+" and "." forms mean "strand" and "frame".
    But how could "+/-/." express strand?
    Does "+" mean the "start-to-end" order and "-" mean "end-to-start" order?
    And how about "."?
    After searching, some other GTF files use "0/1/2" to express frame; however, Cufflinks uses "+/-/." to express.
    Do they match the same meanings?


    Thanks.

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