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Old 04-28-2014, 11:42 AM   #1
WHP
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Default Small RNA Read Counts

New to NGS data, currently analyzing small RNA seq data with emphasis on piRNAs, looking to eventually do differential expression analysis. I have my reads aligned, but now a little unsure of how best to go about getting total read counts for the areas of the genome I am interested in. I have ~500 genomic coordinates for regions of interest which should be areas of piRNA production.

I'm thinking of using bedtools to get a count of alignments which overlap with my ~500 regions. Is there a better way to do this? Suggestions and useful commands/parameters/programs very welcome.

Cheers

Last edited by WHP; 04-28-2014 at 11:53 AM.
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Old 04-28-2014, 01:06 PM   #2
Bukowski
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Default

htseq-count is often used for this.

http://www-huber.embl.de/users/ander...doc/count.html
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Old 12-27-2014, 08:37 PM   #3
vivi-Jasmine
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Quote:
Originally Posted by WHP View Post
New to NGS data, currently analyzing small RNA seq data with emphasis on piRNAs, looking to eventually do differential expression analysis. I have my reads aligned, but now a little unsure of how best to go about getting total read counts for the areas of the genome I am interested in. I have ~500 genomic coordinates for regions of interest which should be areas of piRNA production.

I'm thinking of using bedtools to get a count of alignments which overlap with my ~500 regions. Is there a better way to do this? Suggestions and useful commands/parameters/programs very welcome.

Cheers
Hi, did you resolve your problem? I come across the same question.
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