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-   -   Tophat Exon -intron coverage (http://seqanswers.com/forums/showthread.php?t=29297)

mehtaaditya 04-14-2013 11:07 PM

Tophat Exon -intron coverage
 
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 04-15-2013 02:17 AM

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

mehtaaditya 05-08-2013 09:30 AM

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

hailongcorn 06-19-2014 12:31 AM

Quote:

Originally Posted by mehtaaditya (Post 101719)
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 11-01-2014 03:59 AM

Quote:

Originally Posted by mehtaaditya (Post 104110)
Thanks....... its works..

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


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