SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Using Tophat with low quality Illumina Reads sphil Bioinformatics 5 08-02-2011 08:28 AM
Periodical illumina read length distribution after trimming of low-quality bases luxmare General 4 12-20-2010 04:18 PM
Threshold quality score to determine the quality read of ILLUMINA reads problem edge General 1 09-13-2010 03:22 PM
Reason for low quality of illumina reads nvteja Illumina/Solexa 2 07-07-2010 10:41 AM
How will trimming low-quality ends of Illumina reads affect TopHat and Cufflinks? ecabot RNA Sequencing 1 02-25-2010 09:31 AM

Reply
 
Thread Tools
Old 04-11-2012, 08:21 AM   #1
StephaniePi83
Member
 
Location: France

Join Date: Sep 2011
Posts: 52
Default remove illumina low quality reads

I have to analyse 36 nt long illumina reads.
I use bowtie for 3' end stripping (option -3 <int> ) and then i was wondering if i have to filter reads based on quality ? for example put a threshold and remove reads in wich mean quality value < threshold ... is it possible to do that with bowtie ? if no, how can i do this ?
StephaniePi83 is offline   Reply With Quote
Old 04-12-2012, 04:12 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,079
Default

It is always a good idea to do some QC on your reads before doing alignments.

FastQC is an excellent option (http://www.bioinformatics.babraham.a...ojects/fastqc/). You can also use the Fastx toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
GenoMax 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 02:49 AM.


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