Question: extract only unique mapped paired end reads
gravatar for Mic
3.3 years ago by
Mic70 wrote:


I aligned paired end reads with bwa 0.5.9. Next, I would like to extract only paired end reads which have mapped uniquely to the reference.  How is it possible to do it in Galaxy?

Thank you in advance.



bwa galaxy samtools • 2.8k views
ADD COMMENTlink modified 3.3 years ago by frederik.coppens40 • written 3.3 years ago by Mic70
gravatar for Jennifer Hillman Jackson
3.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:


Tools in the Samtools and Picard groups can filter BAM/SAM datasets, but the best you will be able to do is isolate proper mapped pairs with these methods. Once that is done, you could manipulate the data further with tools in Text Manipulation & Filter and Sort, to look for identifiers that appear only once.

You are likely to miss many good/valid hits with this way of filtering, but I suppose that you know that already. 

Increasing the map criteria is also another way to filter, but reads that multi-map with high quality will also result.

Good luck, Jen, Galaxy team

ADD COMMENTlink written 3.3 years ago by Jennifer Hillman Jackson25k
gravatar for frederik.coppens
3.3 years ago by
VIB, Gent, Belgium
frederik.coppens40 wrote:

BWA gives multimapping reads a mapping quality score of 0, so you can use Filter SAM/BAM and set the minimum MAPQ score on 1

ADD COMMENTlink written 3.3 years ago by frederik.coppens40
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 173 users visited in the last hour