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  • problem of tophat gff file

    Hi all,

    I try to use tophat GFF option, but met some problems. I downloaded the gtf format of Refseq genes from UCSC, and then convert it to gff3 format. But when I feed tophat this file, it returns no junctions were found. I have checked the log file. It has some errors like: "No transcript with id NR_024540".

    Here is NR_024540 gene in my gff3 files:
    Code:
    chr1    hg19_refGene    gene    14363   29370   .       -       .       ID=NR_024540
    chr1    hg19_refGene    mRNA    14363   29370   .       -       .       ID=NR_024540_mRNA;Parent=NR_024540
    chr1    hg19_refGene    exon    14363   14829   .       -       .       ID=NR_024540_exon11;Parent=NR_024540
    chr1    hg19_refGene    exon    14970   15038   .       -       .       ID=NR_024540_exon10;Parent=NR_024540
    chr1    hg19_refGene    exon    15796   15947   .       -       .       ID=NR_024540_exon9;Parent=NR_024540
    chr1    hg19_refGene    exon    16607   16765   .       -       .       ID=NR_024540_exon8;Parent=NR_024540
    chr1    hg19_refGene    exon    16858   17055   .       -       .       ID=NR_024540_exon7;Parent=NR_024540
    chr1    hg19_refGene    exon    17233   17368   .       -       .       ID=NR_024540_exon6;Parent=NR_024540
    chr1    hg19_refGene    exon    17606   17742   .       -       .       ID=NR_024540_exon5;Parent=NR_024540
    chr1    hg19_refGene    exon    17915   18061   .       -       .       ID=NR_024540_exon4;Parent=NR_024540
    chr1    hg19_refGene    exon    18268   18366   .       -       .       ID=NR_024540_exon3;Parent=NR_024540
    chr1    hg19_refGene    exon    24738   24891   .       -       .       ID=NR_024540_exon2;Parent=NR_024540
    chr1    hg19_refGene    exon    29321   29370   .       -       .       ID=NR_024540_exon1;Parent=NR_024540
    Is something wrong with my gff3 file ? does someone have any ideas ?

    Thanks.

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