SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
how --mate-inner-dist and --mate-std-dev affect the tophat mapping result liuxq Bioinformatics 0 11-06-2011 08:53 PM
always reads on plus strand more than on minus strand tujchl Bioinformatics 4 04-29-2011 12:08 AM
different number of reads mapped to plus strand and minus strand gfmgfm Bioinformatics 2 02-03-2011 10:26 AM
RNA-Seq: Multimodal RNA-seq using single-strand, double-strand, and CircLigase-based Newsbot! Literature Watch 0 12-24-2010 02:13 AM
How does inner distances(--mate-inner-dist and --mate-std-dev) work in tophat? Gangcai Bioinformatics 4 06-15-2010 05:53 AM

Reply
 
Thread Tools
Old 09-27-2010, 12:32 AM   #1
valei
Member
 
Location: italy

Join Date: Sep 2010
Posts: 14
Default strand of query and mate

Hi everybody,

I'm performing downstream pair-end analysis on Genome Analyzer II data. The reads was aligned against a reference genome using BWA that gives a BAM output. I'm a novice and I have to understand some basic topic in order to build my pipeline.

For example in the flag field I found 0x0010 (strand of the query) and 0x0020 (strand of the mate); what exactly mean they? I mean, the reads are both given in the forward strand or not? To extract the two sequences readed by GAII, have I to do some transformation (i.e. sense to antisense)??

Thanks!
valei is offline   Reply With Quote
Old 09-27-2010, 04:36 AM   #2
drio
Senior Member
 
Location: 4117'49"N / 24'42"E

Join Date: Oct 2008
Posts: 323
Default

It means exactly that. That flag in your BAM record tells you what is the orientation that the aligner used to map the read. And since you are in a pair-end experiment, the other flag 0x20 comes into play also. It contains the same information but for the other end of the read.
__________________
-drd
drio is offline   Reply With Quote
Reply

Tags
flag, strand

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 08:37 AM.


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