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Old 04-14-2013, 10:07 PM   #1
mehtaaditya
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Location: India

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Default 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.
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Old 04-15-2013, 01:17 AM   #2
NicoBxl
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use intersectbed from bedtools https://code.google.com/p/bedtools/
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Old 05-08-2013, 08:30 AM   #3
mehtaaditya
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Thanks....... its works..
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Old 06-18-2014, 11:31 PM   #4
hailongcorn
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Quote:
Originally Posted by mehtaaditya View Post
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
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Old 11-01-2014, 02:59 AM   #5
Zhan yueping
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Originally Posted by mehtaaditya View Post
Thanks....... its works..
hello,I want to do the same work ! you can tell me more ?
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