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couple of gotchas regarding dot-calling and this snakemake #3

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sergpolly opened this issue Dec 11, 2019 · 0 comments
Open

couple of gotchas regarding dot-calling and this snakemake #3

sergpolly opened this issue Dec 11, 2019 · 0 comments

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@sergpolly
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  1. this thing uses --ignore-diags 1 and a balancing weigh name wsnake - this is really just to be able to later explore different balancing options and their effect on the result (e.g. expected) - so, beware of that wsnake balancing when re-using any intermediate results after running this snake-pipeline
  2. in this snake-pipeline we remove "bad" chromosomes chrM and chrY from expected - these chromosomes are sparse - and they do not yield any dot calls - this messes up the output of the CLI call-dots command, i.e. the final list of significant dots .postproc-one. By mess up I imply genomic coordinates turn float instead of int etc (this is to be fixed on the cooltools-side)

this is based on experiences of @betulakgol @gspracklin

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