SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
paired-end reads mapped to genome.. gene with only one direction of paired-end reads? danwiththeplan Bioinformatics 2 09-22-2011 03:06 AM
RNA-seq remove any reads that map more than 2 times. fabrice Bioinformatics 3 08-17-2011 03:06 AM
SOLiD SAGE reads direction and orientation invermay SOLiD 0 02-14-2011 07:17 PM
cufflinks transcript on wrong strand ornam Bioinformatics 2 12-13-2010 01:33 PM
Single direction reads for variants Moggs General 11 06-22-2010 07:55 AM

Reply
 
Thread Tools
Old 03-01-2012, 02:21 AM   #1
Noa
Member
 
Location: haifa israel

Join Date: Jun 2011
Posts: 62
Default How to remove reads in wrong direction from Cufflinks analysis

I am running sequencing data from a directional RNASeq protocol on bowtie (it is a bacterial genome) and then cuffdiff or cufflinks.
I occasionally see a few reads that align to the wrong direction (opposite strand). Is there any way to filter these out before I do my FPKM analysis?
THanks
Noa
Noa is offline   Reply With Quote
Reply

Tags
cufflinks, directionality, filter, rna-seq

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 09:55 AM.


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