SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Quality Control of Solexa aquleaf Illumina/Solexa 3 04-07-2011 05:15 AM
Quality Control question dicty Bioinformatics 1 02-10-2011 12:58 PM
Quality Control and Quality Values agc Bioinformatics 4 08-23-2010 11:44 PM
Sequence Alignment Quality Control nilshomer Bioinformatics 4 02-06-2010 07:24 AM

Reply
 
Thread Tools
Old 10-07-2011, 01:52 PM   #1
kjaja
Member
 
Location: NY

Join Date: Aug 2011
Posts: 55
Default Quality control steps before alignment?

Hi,

Are any quality control steps that I need do before aligning the reads to the reference genome using the fastq files?
kjaja is offline   Reply With Quote
Old 10-07-2011, 02:09 PM   #2
upendra_35
Senior Member
 
Location: USA

Join Date: Apr 2010
Posts: 102
Default

There are innumerable number of threads related to this top. Try searching......
upendra_35 is offline   Reply With Quote
Old 10-07-2011, 03:53 PM   #3
Heisman
Senior Member
 
Location: St. Louis

Join Date: Dec 2010
Posts: 535
Default

You can look into using FastQC to see if the data set is worth analyzing. Other than that, most QC steps can be implemented after aligning (ie, tossing out reads with high error rates or low mapping qualities, for example).
Heisman is offline   Reply With Quote
Old 10-08-2011, 12:48 AM   #4
simonandrews
Simon Andrews
 
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871
Default

There are some QC steps which would need to be done before aligning. In particular the trimming of any adapter sequences found by QC checks would need to be done early on.

I'd also stress that even if the QC is awful I'd still go ahead and analyse it anyway. We've found biologically interesting results from samples with 97% duplication. When you've got 40 million reads, even if you throw 97% away you still have quite a few left :-)

We view QC as a means to allow us to better evaluate the results of subsequent analysis and to help diagnose problems, rather than a filter to let us throw samples away.
simonandrews 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 06:39 PM.


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