SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
singletons in dexseq_count.py Jetse Bioinformatics 1 12-14-2012 01:05 AM
soapdenovo singletons?? sarbashis De novo discovery 0 04-02-2012 01:39 AM
Removing duplicate reads for tophat? hong_sunwoo RNA Sequencing 2 10-09-2010 01:46 AM
SAM flag field and removing unmapped reads from BFAST output aiden Bioinformatics 3 05-27-2010 07:10 PM
edena singletons agroster Bioinformatics 0 02-01-2010 02:14 PM

Reply
 
Thread Tools
Old 01-21-2013, 02:18 AM   #1
Derek-C
Junior Member
 
Location: U.S.A.

Join Date: Nov 2012
Posts: 7
Default removing singletons from tophat output

Hi all,

I'm trying to get my tophat output without singletons (I'm trying to convert the output back into fastq format so everything needs a mate) but even with both the no-mixed and no-discordant options in tophat, samtools flagstat is still identifying millions of singletons, which are then essentially discarded when converting to fastq. Any ideas?
Derek-C 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 12:29 AM.


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