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Thread Tools |
04-14-2013, 11:07 PM
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#1 |
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Junior Member
Location: India Join Date: Mar 2013
Posts: 9
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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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04-15-2013, 02:17 AM
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#2 |
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not just another member
Location: Belgium Join Date: Aug 2010
Posts: 264
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use intersectbed from bedtools https://code.google.com/p/bedtools/
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05-08-2013, 09:30 AM
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#3 |
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Junior Member
Location: India Join Date: Mar 2013
Posts: 9
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Thanks....... its works..
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06-19-2014, 12:31 AM
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#4 | |
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Junior Member
Location: China Join Date: May 2014
Posts: 6
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Quote:
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11-01-2014, 03:59 AM
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#5 | |
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Junior Member
Location: China Join Date: Oct 2014
Posts: 6
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Quote:
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