Re: [Bio-bwa-help] bwa mem and quality trimming
Status: Beta
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From: Heng Li <lh...@me...> - 2014-02-26 16:10:23
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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 > Dr. Bohr-Gasse 3 > 1030 Vienna, Austria > phone: +436803252197 > ------------------------------------------------------------------------------ > Flow-based real-time traffic analytics software. Cisco certified tool. > Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer > Customize your own dashboards, set traffic alerts and generate reports. > Network behavioral analysis & security monitoring. All-in-one tool. > http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk_______________________________________________ > Bio-bwa-help mailing list > Bio...@li... > https://lists.sourceforge.net/lists/listinfo/bio-bwa-help |