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Question: extract only unique mapped paired end reads
0
gravatar for Mic
3.3 years ago by
Mic • 70
Australia
Mic • 70 wrote:

Hello, 

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.

Mic

 
bwa galaxy samtools • 2.8k views
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modified 3.3 years ago by frederik.coppens • 40 • written 3.3 years ago by Mic • 70
0
gravatar for Jennifer Hillman Jackson
3.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 COMMENT • link written 3.3 years ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for frederik.coppens
3.3 years ago by
frederik.coppens • 40
VIB, Gent, Belgium
frederik.coppens • 40 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 COMMENT • link written 3.3 years ago by frederik.coppens • 40
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