SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Converting FPKM from Cufflinks to raw counts for DESeq jebe Bioinformatics 34 02-05-2014 08:19 AM
Raw read counts for RNAseq biofreak Introductions 13 01-16-2013 05:28 AM
How can one get raw read counts from RPKM values gen2prot General 6 06-24-2011 11:08 AM
DESeq: Read counts vs. BP counts burkard Bioinformatics 0 08-05-2010 11:52 PM
How to convert cufflinks output to raw counts jebe RNA Sequencing 0 01-26-2010 11:29 AM

Reply
 
Thread Tools
Old 06-13-2011, 10:44 AM   #1
biofreak
Member
 
Location: USA

Join Date: Jun 2011
Posts: 44
Default Raw read counts for RNAseq

hi All,
I want to use DESeq package for differential expression analysis.
How do I obtain the raw read counts from each of the SAM files?
thanks.
biofreak is offline   Reply With Quote
Old 06-14-2011, 11:08 AM   #2
d17
Member
 
Location: United States

Join Date: Sep 2008
Posts: 27
Default

Check out Aaron Quinlan's bedtools. The coverageBed utility will get you what you are looking for.
d17 is offline   Reply With Quote
Old 06-15-2011, 05:56 AM   #3
jameslz
Member
 
Location: ShangHai

Join Date: Nov 2009
Posts: 20
Default

htseq-count can also handle it.
http://www-huber.embl.de/users/ander...doc/count.html
jameslz is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 02:36 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO