Question: How do I tell bwa to map only unmapped portion of the read for supplementary alignments?
0
gravatar for Macspider
2.9 years ago by
Macspider3.2k
Vienna - BOKU
Macspider3.2k wrote:

I am using chimeric reads for my analyses, I am asking some questions in a row these days so I hope I'm not getting annoying :D

When bwa mem generates a sam output, it can include supplementary alignments (distinguished by the flag 2048). If I sum up the alignment length of the main alignment and of the supplementary alignment of each read that has one, sometimes I find that it goes beyond the read length.

I would like bwa mem to search for a supplementary alignment only with the unmapped portion of a read: is this possible?

ADD COMMENTlink modified 2.9 years ago by Pierre Lindenbaum131k • written 2.9 years ago by Macspider3.2k
0
gravatar for Pierre Lindenbaum
2.9 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

I would like bwa mem to search for a supplementary alignment only with the unmapped portion of a read: is this possible?

unless I'm missing something, this information would be available in the "SA" tag of the read.

ADD COMMENTlink written 2.9 years ago by Pierre Lindenbaum131k

only with the unmapped portion

This is the interesting part :)

ADD REPLYlink written 2.9 years ago by Macspider3.2k

bu if bwa was able to map this small unmapped fragment, it would be in the SA tag. Why do you expect a new result from BWA ?

ADD REPLYlink written 2.9 years ago by Pierre Lindenbaum131k

Let's say this is the read:

---------------------------------------------------------------

We have perhaps one alignment here:

xxxxxxxxxxxxxxxxxxxxxxxx---------------------------------------

And another here:

------------------------------------------xxxxxxxxxxxxxxxxxxxxx

Putting them together:

xxxxxxxxxxxxxxxxxxxxxxxx---------------------------------------
------------------------------------------xxxxxxxxxxxxxxxxxxxxx

They don't overlap on the read sequence. However, in my dataset I find sometimes situations like this one:

xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx----------------------------
--------------------xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx

Where you can see the overlap in the middle. This means that a region of the read is part of both the "first" alignment and the supplementary alignment. Obviously, I don't want this, because I want each position of the read to be mapped only once.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Macspider3.2k
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