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  • identify single exon transcripts from cufflinks output

    Hey guys,

    Do you have an idea how to identify single exon transcripts from cufflinks output? Dose 'genes with only one exon' means exon_number "1" are eligible?
    The transcripts.gtf file looks like:
    chr1 Cufflinks transcript 11387 11823 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "126581774.1320091337"; frac "1.000000"; conf_lo "23084341.949073"; conf_hi "230079206.314945"; cov "2.510922"; full_read_support "yes";
    chr1 Cufflinks exon 11387 11823 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "126581774.1320091337"; frac "1.000000"; conf_lo "23084341.949073"; conf_hi "230079206.314945"; cov "2.510922";
    chr1 Cufflinks transcript 11874 29043 658 + . gene_id "CUFF.2"; transcript_id "CUFF.2.1"; FPKM "120296038.9757787585"; frac "0.143074"; conf_lo "104144214.907809"; conf_hi "136447863.043749"; cov "2.644528"; full_read_support "no";
    chr1 Cufflinks exon 11874 12227 658 + . gene_id "CUFF.2"; transcript_id "CUFF.2.1"; exon_number "1"; FPKM "120296038.9757787585"; frac "0.143074"; conf_lo "104144214.907809"; conf_hi "136447863.043749"; cov "2.644528";
    chr1 Cufflinks exon 12613 12721 658 + . gene_id "CUFF.2"; transcript_id "CUFF.2.1"; exon_number "2"; FPKM "120296038.9757787585"; frac "0.143074"; conf_lo "104144214.907809"; conf_hi "136447863.043749"; cov "2.644528";
    chr1 Cufflinks exon 13221 29043 658 + . gene_id "CUFF.2"; transcript_id "CUFF.2.1"; exon_number "3"; FPKM "120296038.9757787585"; frac "0.143074"; conf_lo "104144214.907809"; conf_hi "136447863.043749"; cov "2.644528";
    chr1 Cufflinks transcript 11874 14408 1 + . gene_id "CUFF.2"; transcript_id "NR_046018_1"; FPKM "0.0000000000"; frac "0.000000"; conf_lo "0.000000"; conf_hi "6894923.389408"; cov "0.000000"; full_read_support "no";

  • #2
    Something like the following should work:
    Code:
    grep exon transcripts.gtf | awk '{print $10}' | sort | uniq -u
    The will likely give the list of single-exon genes, assuming cufflinks is consistent in its file formatting.

    Edit: I just saw that you wanted single-exon transcripts, not genes. Just change "print $10" to "print $12".

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