Re: [Bio-bwa-help] mem alignment vs aln alignment

[Heng Li <lh...@me...>]

Thanks a lot for the extra information. I can make a guess now: the sequenced sample has a pseudogene not present in the mouse reference genome. Bwa-mem does local alignment, so it can find multiple partial hits for one read. Bwa-aln mostly does semi-global alignment. Even if it can sometimes find one partial hit, it is unable to find both hits to the two exons.

One of the advantages of bwa-mem is that it tells you long-range/structural variations you would not find with most other read mappers. If you are worrying this may complicate downstream analyses, you can consider to filter out hits with long soft/hard clippings.

Heng

On Apr 1, 2015, at 12:56, Saumya Kumar <s....@ha...> wrote:

> I am attaching another slide which has pairing of reads turned on in IGV. Slide 1 is mem and it seems its aligning to nearby exons, but not entirely. Slide2 is aln, also paring turned on.
> 
> Saumya
> 
> -----Original Message-----
> From: Heng Li [mailto:lh...@me...]
> Sent: 01 April 2015 17:49
> To: Saumya Kumar
> Subject: Re: [Bio-bwa-help] mem alignment vs aln alignment
> 
> Second question: in your second slide, where are the other parts of truncated reads mapped? Are they unmapped, mapped to a nearby exon or elsewhere?
> 
> Heng
> 
> On Apr 1, 2015, at 11:38, Saumya Kumar <s....@ha...> wrote:
> 
>> Hi Heng,
>> 
>> For the Slide 1 average read depth is 14 (100bp read length). For slide 2, it's average read depth is 10. (Slide 2 is a different genome with read length as 150bp).
>> 
>> Best,
>> Saumya
>> 
>> -----Original Message-----
>> From: Heng Li [mailto:lh...@me...]
>> Sent: 01 April 2015 14:58
>> To: Saumya Kumar
>> Cc: bio-bwa-help
>> Subject: Re: [Bio-bwa-help] mem alignment vs aln alignment
>> 
>> What is the average read depth across genome?
>> 
>> On Apr 1, 2015, at 5:31, Saumya Kumar <s....@ha...> wrote:
>> 
>>> This is the correct presentation.
>>> 
>>> Thanks, Saumya
>>> 
>>> From: Saumya Kumar
>>> Sent: 01 April 2015 10:30
>>> To: Bio...@li...
>>> Subject: mem alignment vs aln alignment
>>> 
>>> Hello,
>>> 
>>> I have been using BWA-aln for our whole genome paired end data of size about 100bps each. I tried using BWA-mem for the same data and we observe a different kind of alignment when looked up on IGV. It appears to be focussed alignment on exons, appearing as structural variations (please see attached). This difference appears pronounced for whole genome paired end read data of 150 bp (slide 2). Can anyone suggest what might be going on here? All this analysis is done on mouse data.
>>> 
>>> Thanks,
>>> Saumya
>>> 
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