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

[Surya S. <ss...@co...>]

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


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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