Question: Are Some Sequences Uniquely Mapped By Bwa When Mapped As Paired-End That Would Not Be When Mapped As Single-End?
gravatar for KCC
7.3 years ago by
Cambridge, MA
KCC4.0k wrote:

Lets say we have two reads A and B that are paired. Suppose A is uniquely mappable, but B is not uniquely mappable. B maps in two spots. One close to A (say 400 bp) and one far away (100000 bp). Does BWA use that information about proximity to uniquely map B? So mapq > 0 for B in this case.

So, I guess what I'm asking is: are there situations where A and B would have mapq=0 if they were treated as single-end reads, but they have mapq >0 when treated as paired-end, assuming all other things are equal?

The reason I am asking this question is I computed mappability for single-end reads and I noticed that some of my paired-end fragments end in places that shouldn't be uniquely mappable. I used the samtools option to remove reads that have mapq=0, so I think I should only have uniquely mapped reads.

bwa • 3.0k views
ADD COMMENTlink modified 7.3 years ago by lh332k • written 7.3 years ago by KCC4.0k

I am not writing it as an answer because I am not sure about it but I think that BWA uses insert size information if it has to choose out of two alignments for one of the reads. First it aligns each read from a pair independently and stores the first few best matches. It does the same thing for the other read. Finally, depending on the insert sizes it tries to give you the best mapping.

ADD REPLYlink written 7.3 years ago by Ashutosh Pandey12k
gravatar for lh3
7.3 years ago by
United States
lh332k wrote:

Mapping quality measures the chance the read is mismapped. If a pair of read can only be placed at one locus meeting the pairing requirement, both ends are likely to be correct. Mapping quality should be high. Besides bwa, many mappers work this way. For bwa-backtrack, the single-end mapping quality is reported at the SM:i: tag. Bwa-backtrack/bwa-mem may keep thousands of hits when pairing the two ends.

ADD COMMENTlink modified 10 months ago by RamRS28k • written 7.3 years ago by lh332k

A follow up question has been posted here: BWA-MEM - Where has SM:i gone?

ADD REPLYlink written 7.1 years ago by steve40
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