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
>
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