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Re: [Seqan-dev] Paired-end output of RazerS2

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Hi Lingjie,

yes, that issue was on our todo list for a very long time. The occurrence of double hits in paired-end mode with indels is a side effect of overlapping parallelograms of the Swift filter we use in RazerS. In the single-end mode we filter them but in the paired-end it is a bit more involving to detect and correctly filter them. I have found a way this morning which solves the problem easier than I originally thought. Please update to the current trunk of SeqAn and double paired-end hits should be no longer an issue.

Regards,
David
--
David Weese				weese@inf.fu-berlin.de
Freie Universität Berlin		http://www.inf.fu-berlin.de/
Institut für Informatik			Phone: +49 30 838 75246
Takustraße 9					Algorithmic Bioinformatics
14195 Berlin					Room 021 

Am 01.08.2011 um 04:35 schrieb Lingjie Weng:

> Hi,
> 
> I am trying to map some paired-end reads with read length 35 each. The 
> command line I used is :
> 
> ./razers2 --indels --recognition-rate 100 -ll 170 -le 30 --output 
> output.sam hg18.fa 35bp_pe1.fq 35bp_pe2.fq
> 
> RazerS2 reports some alignment twice in the output file.  Do you have 
> any idea of this problem ?
> 
> BTW, if I set max-hits to be 1, then I don't get this problem.
> 
> For your convenience, I attached the read set I used.
> 
> 
> Thanks,
> Lingjie Weng
> <35bp_pe1.fq><35bp_pe2.fq>_______________________________________________
> seqan-dev mailing list
> seqan-dev@lists.fu-berlin.de
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