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  • komais
    Junior Member
    • Apr 2011
    • 5

    #1

    how to convert gtf into bed12

    I download a gene annotation file in gtf format from ensemble, but now , i want to convert it into bed12 format.
    Could anyone provide me some software can convert it easily?

    bed12 format is :
    chr1 90098643 90185094 NM_032270 0 + 90152032 90180541 0 3 238,142,6827, 0,53385,79624,

    gtf format is :

    995283 TIGRannot mRNA 14499 19318 . - . GenePrediction TgTIGRannot_1493 ; ManateeID 31.m00940
    995283 TIGRannot CDS 18785 19318 . - 0 GenePrediction TgTIGRannot_1493
    995283 TIGRannot CDS 18400 18473 . - 0 GenePrediction TgTIGRannot_1493
    995283 TIGRannot CDS 17747 17904 . - 1 GenePrediction TgTIGRannot_1493
    995283 TIGRannot CDS 17089 17220 . - 2 GenePrediction TgTIGRannot_1493
    995283 TIGRannot CDS 16521 16688 . - 2 GenePrediction TgTIGRannot_1493
    995283 TIGRannot CDS 15747 15922 . - 2 GenePrediction TgTIGRannot_1493
    995283 TIGRannot CDS 15201 15299 . - 0 GenePrediction TgTIGRannot_1493
    995283 TIGRannot CDS 14499 14729 . - 0 GenePrediction TgTIGRannot_1493

    The problem is a gene contains many rows in gff file, but it is only in 1 line in bed12.
    I am appreciate if anyone could shed a light on me
  • Chirag
    Member
    • Nov 2011
    • 23

    #2

    Comment

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