SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
BWA: paired end reads, wrong orientation but listed as properly paired rdeborja Bioinformatics 3 06-11-2014 04:39 AM
BWA and paired end reads scami Bioinformatics 2 02-12-2014 11:21 PM
weird output with BWA paired end alignment jmt Bioinformatics 2 08-13-2013 07:05 PM
How exactly do I use BWA with paired-end reads? prs321 Bioinformatics 3 06-17-2013 07:26 AM
BWA alignment for paired end reads AvinashP Genomic Resequencing 2 06-08-2010 04:11 AM

Reply
 
Thread Tools
Old 03-31-2015, 12:46 AM   #1
deepue
Junior Member
 
Location: Europe

Join Date: Mar 2015
Posts: 1
Default BWA alignment using paired end reads from different lanes

Hi,

I would need some help on to proceed for WES analysis.

I observed from different posts in the forum that the paired end reads can be aligned separately and the resulting SAM files are merged for further analysis. I would like to know on how to consider the data from different lanes while doing alignment.

Should i merge the data from different lanes for L{1,2}_R1.fq, L{1,2}_R2.fq into separate files or perform alignment for different read type(1,2) and different lanes specific data separately(4 times L1_R1.fq, L1_R2, L2_R1, L2_R2) and merge the SAM files for further analysis ?

Please advise.

Thanks
deepue is offline   Reply With Quote
Old 03-31-2015, 01:40 AM   #2
lindenb
Senior Member
 
Location: France

Join Date: Apr 2010
Posts: 143
Default

cross posted: https://www.biostars.org/p/136497/
lindenb is offline   Reply With Quote
Reply

Tags
bwa, lane, paired end reads

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 11:48 PM.


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