Re: [Bio-bwa-help] bwa mem and quality trimming

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

You can align reads with many adapter sequences. Bwa-mem will just soft clip them (again, bwa-backtrack will have problems). However, it is still recommended to trim adapter sequences. After all, adapters are not part of the samples you are sequencing. They might affect variant calling in corner cases.

Heng

On Feb 26, 2014, at 11:16 AM, Chris Penkett <cj...@ca...> wrote:

> 
> Hi all,
> 
> Thanks, this is useful to know!  Is it worth to do adapter trimming 
> before BWA mem?
> 
> Best wishes
> Chris
> 
> 
> 
> On 26/02/14 16:09, Heng Li wrote:
>> You don’t need to do quality trimming with bwa-mem. BWA-backtrack requires reads to be mapped in full length. Low-quality tail may greatly affect its sensitivity. Bwa-mem largely does local alignment. If a tail cannot be mapped well, it will be soft clipped.
>> 
>> Heng
>> 
>> On Feb 26, 2014, at 5:35 AM, Hannes Svardal <ha...@sv...> wrote:
>> 
>>> Hi all,
>>> 
>>> I was searching in the mailing list archives,
>>> but I could not find any satisfactory reply to my issue so I would like to post it here.
>>> 
>>> I have Illumina 100bp paired end reads and want to align them to a reference genome. With bwa aln there was the -q option to trim low quality ends of reads on the fly.
>>> 
>>> Now bwa mem does not provide such an option. Does it deal with low quality parts of the reads automatically, or should the reads be trimmed beforehand?
>>> Note that I am not talking about adapter trimming, those should have been removed beforehand in any case.
>>> 
>>> If quality trimming is recommended, I am not clear as to whether reads that are below 70bp in length should be discarded after trimming. (It is noted that bwa mem is only recommended for reads >=70bp.) Does anyone have an answer to this?
>>> 
>>> In particular, I used trimmomatic to trim if the average quality over 4bp windows is below 15. I often get read pairs where one mate is discarded due to length<70bp after trimming. In this case I would have to map single reads. Intuitively, I have the feeling that the alignment of a 100 bp read could be facilitated by having a mate, even if the mate is only 50bp after trimming. Should I keep pairs where one mate is <70 bp and the other >70bp or does bwa mem have troubles with this?
>>> 
>>> Thanks a lot in advance,
>>> Hannes
>>> 
>>> PS.: There is a related discussion here, but no satisfactory reply:
>>> http://www.biostars.org/p/90149/#90184
>>> 
>>> -- 
>>> Dr. Hannes Svardal
>>> Postdoctoral researcher
>>> Nordborg group
>>> 
>>> Gregor Mendel Institute
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> 
> -- 
> Bioinformatician
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> 
> 
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