Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
strand bias P-value lyz1030 Bioinformatics 1 07-16-2012 01:12 AM
Illumina DNA sequence specific strand bias involving orphan reads Tally Bioinformatics 1 06-21-2012 06:26 AM
strand bias zorph Bioinformatics 0 06-13-2012 03:44 PM
Evidence of Strand Bias AnamikaDarwin Bioinformatics 1 06-27-2011 05:21 PM
Forward strand bias? dawe Bioinformatics 6 04-05-2010 08:00 AM

Thread Tools
Old 09-06-2012, 06:13 AM   #1
Location: london, uk

Join Date: Nov 2010
Posts: 4
Default fundamental strand bias in sequence data

Does anyone else see fundamental strand bias in many mapped read positions. That is, for exome sequencing I see both reference allele and variant allele in one particular stand only, can be either + or - strand, for many cases, as if only one strand has been aligned or sequenced at those positions? I am using casva 1.8 to align and then resulting BAM files processed with samtools (sort and mpileup) and varscan.

kingsalex is offline   Reply With Quote
Old 09-07-2012, 12:44 AM   #2
Location: Barcelona

Join Date: Aug 2010
Posts: 12

I'm not familiar with exome sequencing, but I would suspect that the strategy used to enrich the sample in exons may have introduced that bias.
Lluc is offline   Reply With Quote
Old 12-12-2013, 07:52 AM   #3
Location: USA

Join Date: Mar 2010
Posts: 49

In any capture data the regions farthest from the probes tend to have single stranded coverage if the read length is shorter than the insert length.
m_two is offline   Reply With Quote

casava 1.8, strand bias, varscan

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 04:16 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO