SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Bowtie 2 parameters, how does this make sense KnowNothing2 Bioinformatics 3 12-10-2013 11:01 AM
why the properly paired results from bwa mem is an odd number Pengfei Liu Bioinformatics 2 08-24-2013 06:26 PM
Consensus genotypes of SOAPsnp make no sense skblazer Bioinformatics 0 11-27-2012 01:21 PM
How to make sense of Tophat's output file 'junctions.bed' gsinghal RNA Sequencing 4 09-03-2012 06:49 AM
Can anyone make sense of the quality scores in the qseq.txt files? TylerBackman Bioinformatics 2 04-29-2009 09:23 AM

Reply
 
Thread Tools
Old Yesterday, 04:00 AM   #1
martipujolar
Junior Member
 
Location: aarhus, denmark

Join Date: Aug 2018
Posts: 1
Default cannot make sense of BWA MEM results, help!!

hi, been using both Bowtie2 and BWA mem with sequencing data from different species
Bowtie 2 results make sense, since I get a higher % of aligned reads when comparing to the species that is closer phylogenetically (50%) relative to other 2 species which are less related (25%)

However, when I use BWA mem, I get a higher but similar % of alignment with all 3 sp, around 85%. Much higher number of alignments but does not make sense from a phylogenetic point of view. I am using the default options in BWA mem.

Anyone have any thoughts? ideas? would be much appreciated
martipujolar 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 05:24 PM.


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