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  • Problem with Cufflinks output

    Hello,

    I have an unusual problem with my cufflinks output- namely, the transcripts.gtf file. I am getting absolutely nothing except single exon transcripts- that is to say, alternating, exactly identical, transcript and exon lines.

    chr10 Cufflinks transcript 83619 83674 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; FPKM "36911.0556109675"; frac "1.000000"; conf_lo "17181.266485"; conf_hi "56640.844737"; cov "11187.769082"
    ;
    chr10 Cufflinks exon 83619 83674 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "36911.0556109675"; frac "1.000000"; conf_lo "17181.266485"; conf_hi "56640.844737"; cov "1118
    7.769082";
    chr10 Cufflinks transcript 282744 282905 1000 . . gene_id "CUFF.2"; transcript_id "CUFF.2.1"; FPKM "138.1416037618"; frac "1.000000"; conf_lo "58.385512"; conf_hi "217.897696"; cov "41.870825";
    chr10 Cufflinks exon 282744 282905 1000 . . gene_id "CUFF.2"; transcript_id "CUFF.2.1"; exon_number "1"; FPKM "138.1416037618"; frac "1.000000"; conf_lo "58.385512"; conf_hi "217.897696"; cov "41.870825";
    chr10 Cufflinks transcript 284290 284502 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "112.5216564869"; frac "1.000000"; conf_lo "68.387032"; conf_hi "156.656281"; cov "34.105400";
    chr10 Cufflinks exon 284290 284502 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "112.5216564869"; frac "1.000000"; conf_lo "68.387032"; conf_hi "156.656281"; cov "34.105400";

    This is true of every single line in the file as far as I can tell. I must be using Cufflinks wrong somehow. I am giving it a .sam file that appears fine to me (these are just the first few lines):

    HWI-EAS146:5:22:767:1788#0/1 0 chr10 56766 0 46M * 0 0 ATCTATGACAAACCCACAGCCAACATAATACTGAATGGGGAAATGG BABBCBCC@BBBBBAAB?CBBBBBBABBBAAAB@@?B@BA<?@BBB MF:i:0 NM:i:1 UQ:i:30 H0:i:85 H1:i:20
    HWI-EAS146:5:33:824:1624#0/1 0 chr10 57275 0 46M * 0 0 GCGCATGCCTATAATCCCAGCTACTCGGGAAGCTGAGGCAGGAGAA :;BAA7A@AAB<BB?A7;;?;?<?2:ABA?>A0.:=A<99>=-:9: MF:i:0 NM:i:0 UQ:i:0 H0:i:85 H1:i:85
    HWI-EAS146:5:94:1137:48#0/1 0 chr10 73352 0 46M * 0 0 CAACTAACGAGCAAAATAACCAGCTAACATCATCATGACAGGATCA A3@:A>?BA>A>5=5>B<ABA;9B><<@@?49B95?425=6>-?>= MF:i:0 NM:i:0 UQ:i:0 H0:i:85 H1:i:85
    HWI-EAS146:5:93:873:1598#0/1 16 chr10 83093 0 46M * 0 0 GCTCTCGGCCTCGGTGAACTCCATCTCATCCATGCCCTCGCCCGTG 4=AB?A>A>B?B<?9A>6ABAA<5BABA?@B@4BBBBBBBBBB3BB MF:i:0 NM:i:1 UQ:i:30 H0:i:0 H1:i:10
    HWI-EAS146:5:100:436:1980#0/1 0 chr10 83484 0 46M * 0 0 GCCCGGTACTGCTGGCTGCCCCGGCTGGGCAGGGGGGCAAAGCCGG ABBBBB>BBABB?BBBA@-:A>9=%%%%%%%%%%%%%%%%%%%%%% MF:i:0 NM:i:2 UQ:i:8 H0:i:12 H1:i:4
    HWI-EAS146:5:16:1349:1063#0/1 0 chr10 83485 1 46M * 0 0 CCCGGTACTGCTGGCTGCCCCGGCTGGTCAGTGGGGCAAAGCCGGG BBB=?>BBABBA?@B@B<<A@2=8):%%%%%%%%%%%%%%%%%%%% MF:i:0 NM:i:0 UQ:i:0 H0:i:12 H1:i:4

    Do you have any idea what could be causing this unsual output?

    Thank you in advance!

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