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open2c / pairtools

Extract 3D contacts (.pairs) from sequencing alignments
MIT License
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Add summaries #105

Closed Phlya closed 2 years ago

Phlya commented 3 years ago

Adding first support for summary statistics: for now just fraction of cis reads (at all currently calculated minimal separations) and library complexity estimate.

Phlya commented 2 years ago

What would make sense to do with complexity estimates after merging?.. I think it depends on whether the merged files are separate "lanes" from the same library (then it should be just recalculated from merged duplicates/total mapped reads), or whether the pairs come from different replicates (then they should be summer up, perhaps?). So do we need an argument for that?

agalitsyna commented 2 years ago

@Phlya How about throwing a warning if "merge" command is in the header?