Re: [Bio-bwa-help] help on inconsistent CIGAR and read length again
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From: Heng Li <lh...@sa...> - 2013-11-20 15:34:47
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It is nontrivial for me to find the right example that triggers the bug. Without reproducing the bug at my own hand, it is very hard to fix it. Could you reproduce the bug on a small data set and send it to me? Thanks a lot, Heng On Nov 20, 2013, at 10:24 AM, David A. <das...@ho...> wrote: > Dear Heng and Kai > > thanks ever so much for your prompt answer. I really appreciate it. > > Heng, we are planning on upgrading to BWA MEM, but do you mean that you can run bwa aln for 300bp paired-end design using -e flag on an amplicon setting and then do bwa sampe without any CIGAR errors? I am not able to generate the bam file from bwa sampe because of the CIGAR error. > > Kai, I was under the impresion from SEQAnswers that Pindel would work on overlapping reads as long as the alignment coordinates were modified by hand (see post #12 on thread http://seqanswers.com/forums/showthread.php?t=8293) , but maybe the new version of Pindel, which I have not checked yet, has included changes to allow overlapping paired en reads. > > Best, > > Dave > > Subject: Re: [Bio-bwa-help] help on inconsistent CIGAR and read length again > From: lh...@sa... > Date: Tue, 19 Nov 2013 10:00:11 -0500 > CC: bio...@li... > To: das...@ho... > > I cannot reproduce the CIGAR bug at my hand. It is very difficult for me to fix it. For 200bp reads, bwa mem should be better. The default setting is able to align 60bp indels, up to ~95bp given 200bp reads. Tuning the parameters may give you >100bp indels. I am also thinking if I should change the default setting to allow long indels. > > Heng > > On Nov 19, 2013, at 9:25 AM, David A. <das...@ho...> wrote: > > Dear list, > > we have recently moved to the new illumina chemistry to obtain 300bp reads. We are performing amplicon sequencing and our amplicons range from about 230 nt to 400 nt long. > > With the previous chemistry, and 200nt long reads we performed alignment using bwa aln with flag -e set to 60 value trying to capture large indels. And the analysis went fine. > > Now with the new fastq files, we cannot use this -e flag because the CIGAR and the read length are inconsistent. See example: > > Sequence length 301 vs 296 from CIGAR > > We are using the latest release from BWA 0.7.5a r405. I believe that this could be due to the fact that some reads are aligning over adjacent contigs since BWA concatenates all references into one long DNA chunk, could it be so? > > Is it possible to overcome this issue? How can I make sure that one read aligns to one reference and not to two? Because if I am not wrong, for BWA MEM and BWA-SW we can use the -M flag to avoid this, right? > > Also, we are looking into trying BWA MEM and BWA SW but these two tools do not seem to be able to accomodate for long indels, is this correct? How could I allow gapped alignment for large indels? > > Thanks ever so much for your help. > > Dave. > ------------------------------------------------------------------------------ > Shape the Mobile Experience: Free Subscription > Software experts and developers: Be at the forefront of tech innovation. > Intel(R) Software Adrenaline delivers strategic insight and game-changing > conversations that shape the rapidly evolving mobile landscape. Sign up now. > http://pubads.g.doubleclick.net/gampad/clk?id=63431311&iu=/4140/ostg.clktrk_______________________________________________ > Bio-bwa-help mailing list > Bio...@li... > https://lists.sourceforge.net/lists/listinfo/bio-bwa-help > > > = -- The Wellcome Trust Sanger Institute is operated by Genome Rese= arch Limited, a charity registered in England with number 1021457 and a = company registered in England with number 2742969, whose registered = office is 215 Euston Road, London, NW1 2BE. > = -- The Wellcome Trust Sanger Institute is operated by Genome Rese arch Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. |