Dear Nils and Mike, Mike: bedtools intersect does indeed the job, only for single-end BAMs though (as Nils mentioend). bedtools pairtobed also does the job (almost), except that mapQ filtering and readGroup tags filtering requires additional steps. More importantly, though, I see that if I have an rRNA region in a region spanned by a spliced read (so the read itself does not overlap with the rRNA and the rRNA lies between the two parts of the splice), bedtools still considers this an overlap (which is not what I have in mind). Thanks for the tip, still, I think I could use more of pairtobed in other cases :).
Nils: I have been looking to htsjdk in fact (thanks to all who has developed it ~ looks very nice) and I will let you know if I come across anything :). Cheers, Bow On Wed, Oct 1, 2014 at 3:27 AM, Mike Lindberg <[email protected]> wrote: > If you want to get rid of the pair used bedtools pairtobed -a bam -b > rRNA.bed -type either > There are other options in pairtobed you can use and the bam automatically > get changed into bedpe format where you can then filter on mq. > > On Sep 30, 2014, at 9:18 PM, Nils Homer wrote: > > Hey Bow, > > unfortunately there is no single tool that would perform your task. While > you could try to chain various tools together, the difficulty in this > process is to make sure that the mate information for paired reads is > updated correctly. If you want some tips on developing such a tool for your > own use, I would be happy to discuss this off-list, > > N > > On Mon, Sep 29, 2014 at 6:56 AM, Wibowo Arindrarto <[email protected]> wrote: >> >> Dear samtools list, >> >> I was wondering if the Picard suite has a tool to wipe reads from a >> BAM file given a list of targeted regions? >> >> My use case is to remove all reads mapping to known ribosomal RNA >> regions. While there are tools to do simple reads removal out there >> (e.g. bedtools), what I am looking for is to have as if the reads in >> the given region were never mapped in the first place. For example, if >> read01 maps to a ribosomal RNA gene and another gene, the tools would >> remove read01 from both the rRNA gene and the other gene (taking into >> account pairing structure, MAPQ values, and others of course). >> >> I have been browsing around the Picard website to find such a tool, >> and the most close I can find is the FilterSamReads tool. So just to >> double-check in case I may be reinventing something, I am wondering if >> someone has developed something like this :). >> >> Best regards, >> Bow >> >> >> ------------------------------------------------------------------------------ >> Slashdot TV. Videos for Nerds. Stuff that Matters. >> >> http://pubads.g.doubleclick.net/gampad/clk?id=160591471&iu=/4140/ostg.clktrk >> _______________________________________________ >> Samtools-help mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/samtools-help > > > ------------------------------------------------------------------------------ > Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer > Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports > Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper > Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer > http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk_______________________________________________ > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help > > ------------------------------------------------------------------------------ Meet PCI DSS 3.0 Compliance Requirements with EventLog Analyzer Achieve PCI DSS 3.0 Compliant Status with Out-of-the-box PCI DSS Reports Are you Audit-Ready for PCI DSS 3.0 Compliance? Download White paper Comply to PCI DSS 3.0 Requirement 10 and 11.5 with EventLog Analyzer http://pubads.g.doubleclick.net/gampad/clk?id=154622311&iu=/4140/ostg.clktrk _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
