Re: [MUMmer-help] delta-filter parameters for out of order matches

[Adam P. <aph...@gm...>]

Hi Surya,
See if the delta-filter -g option does what you want. That option will
enforce that the relative ordering of alignments on both the reference and
query is consistent.

Best,
-Adam


On Wed, Feb 11, 2015 at 1:24 PM, Surya Saha <ss...@co...> wrote:

> Hi Adam et al.,
>
> I am trying to use nucmer/delta-filter (v3.23) to align BACs to a
> chromosome with gaps (Ns) with a goal to find BACs that span gaps. I want
> to filter out any imperfect alignments. This also means any BAC that aligns
> out of order on the chromosome.
> Here is an example with out of order alignments (100% identity)
> BAC:100-200 aligns to CHR:500-600
> BAC:201-300 aligns to CHR:1001-1100
> BAC:301-400 aligns to 701-800
>
> I am trying to optimize delta-filter parameters for screening these out. I
> can screen out all alignments where a region of the chromosome is covered
> by multiple BACs with -u (99-100). Any ideas how to screen out the out of
> order alignments with delta-filter? Thanks!
>
>
> -Surya
>
>
> --
>
> Surya Saha
> Sol Genomics Network,
> Boyce Thompson Institute, Ithaca, NY, USA.
> Plant Pathology and Plant-Microbe Biology Section,
> Cornell University, NY, USA.
> http://www.linkedin.com/in/suryasaha
> https://twitter.com/SahaSurya
>
>
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