SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
quality value of fastq file and tophat narges Bioinformatics 4 09-16-2012 05:04 AM
Sort fastq files in order of quality? naragam Bioinformatics 6 07-02-2012 04:56 AM
smallRNA GAIIx raw fastq files - quality filter? vebaev Bioinformatics 0 08-22-2011 10:30 AM
quality filtered illumina PE reads Wallysb01 Bioinformatics 1 07-21-2011 10:04 AM
BWA mapping fastq files with Illumina quality maricu Bioinformatics 3 11-19-2010 11:18 AM

Reply
 
Thread Tools
Old 11-28-2012, 03:59 AM   #1
bob-loblaw
Member
 
Location: /home/bob

Join Date: Jun 2012
Posts: 59
Default Using quality filtered fastq files with TopHat

Hi all,
I want to use tophat with my paired-ends RNA-Seq data, which are in fastq format. The problem however is that after I quality filter my files using the fastx-toolkit, the reads are no longer in the same order in each paired end file and so will not run in tophat. Sorting my reads could prove to be a bit of a challenge too, each PE file is 20gb + with 100 million + reads. I was wondering if anyone had a similar problem and knew of a work around? I was thinking about using the raw data files in tophat (Which to my knowledge are in the proper order) and quality filtering afterward, although I'm not sure how much of an issue that would be?
bob-loblaw is offline   Reply With Quote
Old 11-28-2012, 04:25 AM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480
Default

It may prove easier to quality filter/trim with a tool that can directly handle paired-end reads. Look into trimmomatic or trim_galore (I find it to be convenient), among likely others.
dpryan is offline   Reply With Quote
Old 11-28-2012, 05:44 AM   #3
bob-loblaw
Member
 
Location: /home/bob

Join Date: Jun 2012
Posts: 59
Default

Quote:
Originally Posted by dpryan View Post
It may prove easier to quality filter/trim with a tool that can directly handle paired-end reads. Look into trimmomatic or trim_galore (I find it to be convenient), among likely others.
Great, thanks. I'll look into that.
bob-loblaw is offline   Reply With Quote
Reply

Tags
fastq, fastx toolkit, paired-ends, 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 01:33 PM.


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