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From: Surya S. <ss...@co...> - 2015-02-11 18:25:00
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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 |