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
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
Comment