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mskilab-org / chromunity

Discovery of communities in Pore-C concatemers
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Duplicate binsets? #4

Open kyrgyzstanygnacio opened 2 years ago

kyrgyzstanygnacio commented 2 years ago

Hello,

I've run sliding window Chromunity at 25 kb resolution. Looking at the results, I noticed that there are some binsets with identical ranges, but they were called in adjacent, overlapping windows so their binid/chid differ. When I look at their concatemers, some duplicated binsets have the same reads mapped to them, but others have different reads. How do you suggest handling these duplicates for synergy and other downstream analyses (e.g. comparing methylation in synergistic vs non-synergistic regions)?

Thank you!

asd1289 commented 2 years ago

HI @kyrgyzstanygnacio . Sorry for delayed response. In current implementation we consider them separate bin-sets. The reason why you see different sets of concatemers is because as an optimization step, chromunity only looks at concatemers in the window under consideration. I will suggest you can keep them separate as these should be a small subset of all called bin-sets.