Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
RG tags in merged BAM files, muliple lanes one sample cow_girl Bioinformatics 17 08-27-2013 11:28 PM
Design of expt across multiple lanes jbono RNA Sequencing 2 05-15-2013 10:13 AM
aligning multiple fastq for the same sample epi Bioinformatics 16 05-11-2012 12:10 PM
The best to process sample with 2 lanes of data? foxyg Bioinformatics 2 01-06-2011 02:25 PM
Input to BWA from multiple Lanes AvinashP Bioinformatics 2 06-11-2010 08:24 AM

Thread Tools
Old 05-29-2013, 04:11 AM   #1
Senior Member
Location: US

Join Date: Aug 2011
Posts: 105
Default Same sample - multiple lanes

Hi all,
I am doing some whole genomes. Each sample (2 samples, so 24 lanes in total) was run using 12 lanes of a solid5500 machine. for the post-sequence analysis, I have aligned each lane individually, and my question is this:

Is it better to merge all 12 of the individual alignments together and then do the indel realign and base reaclibration on 1 large file? I have been trying this, but I can't seem to get through the base-recalibration step as the program fails due to an error of not having enough memory.

Or can I do the indel realign and base reaclibration on each individually aligned lane, and then merge everything together after all of this is complete?

I suspect that option 1 is the best approach but probably computationally the most expensive. Any thoughts would be appreciated.
lre1234 is offline   Reply With Quote

baserecalibrator, indelrealigner, wgs

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 07:45 PM.

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