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Scott-Devine / MELT-LRA

MELT-LRA: Mobile Element Insertion Site Classifier
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Revisit/revamp coverage calculation #26

Closed jonathancrabtree closed 11 months ago

jonathancrabtree commented 1 year ago

The current coverage calculation doesn't look strict enough. We're looking at coverage (roughly) in terms of (last_base_aligned_with_ME - first_base_aligned_with_ME) / insertion_length (and also discounting polyA/TSD, although that's not the main issue.) So we get something like this with ~92% coverage but the real number is clearly lower:

Screen Shot 2023-09-11 at 10 07 40 AM

Try a strict % bases covered and see what it does to the results.

jonathancrabtree commented 11 months ago

old percent coverage = 97.1%, new = 78.1%:

Screen Shot 2023-10-20 at 12 07 03 PM

jonathancrabtree commented 11 months ago

old percent coverage 97.5%, new = 73.7%:

Screen Shot 2023-10-20 at 12 09 36 PM