Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Best RNA-seq program for unpaired reads reshetovdenis RNA Sequencing 15 02-02-2012 01:18 AM
How to count Paired-End reads for RNA-Seq read counts epistatic RNA Sequencing 0 08-31-2011 03:44 PM
Unpaired reads in paired data Nick General 0 06-22-2011 08:19 AM
RNA-seq with paired-end reads xuying RNA Sequencing 9 09-11-2009 04:00 PM

Thread Tools
Old 05-14-2010, 03:15 PM   #1
Location: California

Join Date: Apr 2010
Posts: 10
Default RNA-Seq analysis with paired and unpaired reads

I would like to compare the expression of two samples, one contains 60 million unpaired reads and the other contains 40 million unpaired reads and 20 million paired-end reads. What software would people recommend to use to find genes/transcripts that are differentially expressed? I have used tophat/cufflinks/cuffdiff on the unpaired reads. Can I use it utilize both paired and unpaired reads?
bzhang is offline   Reply With Quote

cuffdiff, paired-end, rna-seq, tophat

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 06:53 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO