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  • cufflinks assemble

    Hi everyone

    I assembled my RNA_seq data using tophat and cufflinks. But the assemble result seems strange. The length of exons were very short and most time, one transcript only contains one exon. I ran tophat and cufflinks using the default parameters, did I do something wrong? Here is some examples:

    chr1 Cufflinks exon 1374518 1374621 1000 . . gene_id "CUFF.1"; transcript_id "CUFF.1.1"; exon_number "1"; FPKM "901
    .2568132303"; frac "1.000000"; conf_lo "0.000000"; conf_hi "2373.585808"; cov "0.389115";
    chr1 Cufflinks transcript 2986172 2986198 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; FPKM "6948.5151239
    471"; frac "1.000000"; conf_lo "0.000000"; conf_hi "14971.969279"; cov "3.000000";
    chr1 Cufflinks exon 2986172 2986198 1000 . . gene_id "CUFF.3"; transcript_id "CUFF.3.1"; exon_number "1"; FPKM "694
    8.5151239471"; frac "1.000000"; conf_lo "0.000000"; conf_hi "14971.969279"; cov "3.000000";

    do you have some idea about that?

    thanks

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