Re: [Bio-bwa-help] xa2multi.pl mate pair info

[Cittaro D. <cit...@hs...>]

On Aug 27, 2012, at 9:50 PM, Erik Aronesty <er...@q3...> wrote:

> Definitely not looking & forging ahead.  xa2multi is a simple script, only useful for pipelines that ignore lots of things (like proper pairing, etc).
>
> I have a working version that:
>
> - calculates fragment distribution
> - preserves and optimizes mate pairs for multiple alignments using the fragment distribution
> - removes incorrect/false alignments
> - fixes bit flags
>

Mmmm, I'm interested in this one... I have a sample with lots of multiple matching reads, in paired-end and I was just thinking to a strategy to handle those alignments...

> if you want it
>
> - Erik
>
> On Mon, Aug 27, 2012 at 2:11 PM, Nicholas Stong <ne...@gm...> wrote:
> I'm trying to look at multiply mapped reads using bwa, but as far as I can tell the most recent version of xa2multi.pl does not properly set the RNEXT and PNEXT sam fields.  I've found several programs that incorporate xa2multi.pl into their pipelines.  Are they just not looking at those fields and forging ahead, or is there something I'm missing?
>
> Thanks,
>   Nick
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Bio-bwa-help mailing list
> Bio...@li...
> https://lists.sourceforge.net/lists/listinfo/bio-bwa-help
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
> Bio-bwa-help mailing list
> Bio...@li...
> https://lists.sourceforge.net/lists/listinfo/bio-bwa-help

/*
Davide Cittaro, PhD

Coordinator of Bioinformatics Core
Center for Translational Genomics and Bioinformatics
Ospedale San Raffaele
Via Olgettina 58
20132 Milano
Italy

Office: +39 02 26439140
Mail: cit...@hs...
Skype: daweonline
*/












--------------------------------------------------------------------------
LA TUA CURA E' SCRITTA NEL TUO DNA. AL SAN RAFFAELE LA STIAMO REALIZZANDO.
AIUTA LA RICERCA, DAI IL TUO 5XMILLE - CF: 03 06 80 153
info:www...@hs... - www.5xmille.org

Disclaimer added by CodeTwo Exchange Rules 2007
http://www.codetwo.com