SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
SNP flanking regions with "pseduo"-reference & viewing all alignments around SNPs fox454 Bioinformatics 2 10-30-2015 09:46 AM
BWA-MEM non-primary alignments "false proper pairing" kartong Bioinformatics 5 08-18-2014 11:29 PM
Samtools mpileup - why does it call an "N" when there ARE correct alignments? TabeaK Bioinformatics 3 01-07-2013 08:33 AM
"refine gapped alignments... Segmentation fault" while using bwa sampe dd_genome Bioinformatics 3 01-03-2013 10:42 AM
Peak finding with MACS: Questions on # of reads and "strand bias" jjw14 Bioinformatics 0 07-29-2010 06:17 AM

Reply
 
Thread Tools
Old 01-10-2018, 09:17 AM   #1
sdriscoll
I like code
 
Location: San Diego, CA, USA

Join Date: Sep 2009
Posts: 438
Default Is finding "all" alignments a pipe dream?

All is a bit arbitrary, of course, so maybe I just mean "all within a certain alignment quality boundary". I've wrestled with this time and time again - it seems that no matter how I tweak an aligner's settings I can always take the unaligned reads and run through another aligner, against the same reference, and find more alignments. Often there are really good alignments in that results so it's not just that one aligner can find alignments with more errors that the first failed to find.

Maybe even more of an issue is with certain multi-mappable reads. I might have one aligner only give me a few alignments while another gives me dozens. I know how to use aligners well enough to understand how to control multi-mapping so I'm sure it's not just because I have them set differently. More often than not I want to know if a read maps to multiple loci or not and if so does it map to A LOT of loci to the point that it's a read that I want to discard.

The best solution I can come up with is to use a consensus type of approach. Run multiple aligners, maybe even with different settings (for instance running BBMap with '-slow' and '-vslow' picks up additional alignments that it misses when using mostly standard settings), pooling said alignments, remove redundant alignments, and move on from there. I really don't want to do that due to the amount of time it will take running all of those alignments but it seems like there's just no single pass solution that works.

Comments?
__________________
/* Shawn Driscoll, Gene Expression Laboratory, Pfaff
Salk Institute for Biological Studies, La Jolla, CA, USA */
sdriscoll 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 09:00 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO