Filtering nets for best alignment in target

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Coelho De Almeida, Pedro

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Apr 18, 2018, 11:57:02 AM4/18/18
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Hi,

I’m trying to align 2 whole genomes and am following the procedure described in this wiki page http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto. Basically, I’ve done the axtChain | chainMergeSort | chainPreNet | chainNet | netSyntenic  pipeline. I would now like to filter out, i.e. exclude from the net file, overlapping alignments in the target sequence, keeping only the best one in terms of alignment score, and also to remove other alignments that for example are shorter than 30% for that aligned query.

I looked at `netFilter` and `netChainSubset` but don’t think they would do what I want. I could try to write some parser myself but was wondering if this is something that is already available and that I have missed.

Thanks,
Pedro

Christopher Lee

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Apr 18, 2018, 7:58:37 PM4/18/18
to Coelho De Almeida, Pedro, gen...@soe.ucsc.edu
Hello Pedro,

Thank you for your question about whole genome alignments and
filtering your net file. Can you provide an example of these
overlapping alignments on the target sequence that you would like to
filter? Nets are by definition single coverage on the target, although
lower level chains may be used to "fill in" gaps in the top level
chain.

Thanks,

Christopher Lee
UCSC Genomics Institute
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