Tophat Exon -intron coverage

[mehtaaditya]

Hi everyone
i mapped my high quality reads on my reference genome using Tophat 2.0.7 ver. Now i want to know how many reads fall (mapped) in my exon and intron regions. and how many reads fall in intergenic regions. i stucked this place. Is anybody know how can i get exon intron and intrgenic reads mapping from my mapping file. Any suggestions will appreciate. Thanks in advance.

[NicoBxl]

use intersectbed from bedtools https://code.google.com/p/bedtools/

[mehtaaditya]

Thanks....... its works..

[hailongcorn]

Hi everyone
i mapped my high quality reads on my reference genome using Tophat 2.0.7 ver. Now i want to know how many reads fall (mapped) in my exon and intron regions. and how many reads fall in intergenic regions. i stucked this place. Is anybody know how can i get exon intron and intrgenic reads mapping from my mapping file. Any suggestions will appreciate. Thanks in advance.

hello,I want get exon intron and intrgenic file,how can i get this from tophat bam or bed file?Thank you

[Zhan yueping]

Thanks....... its works..

hello，I want to do the same work ! you can tell me more ?