Could the minimum default length for identifying a candidate IES by MILRAA (25 bp) be reduced?

Swart-lab / bleties

IES retention analysis from PacBio CCS reads

https://swart-lab.github.io/bleties

MIT License

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Could the minimum default length for identifying a candidate IES by MILRAA (25 bp) be reduced? #2

Closed gh-ecs closed 3 years ago

gh-ecs commented 3 years ago

Here's a nested 18 bp candidate:

Would one get a lot of false positives if one were to chose, e.g. a value of 15?

kbseah commented 3 years ago

We could definitely run it with a lower value and see what happens. I think the minimum coverage would be more important in filtering out false positives

gh-ecs commented 3 years ago

I've dropped it to 15 bp now, and get a few extra putative IESs per contig - most of which look quite plausible (as far as I can tell). Some are 15 bp, so perhaps we can go even lower... Interesting, since Paramecium's shortest IESs are 26 bp. I wonder how short we can go (trying 8 bp now)...

kbseah commented 3 years ago

Default is now 15, closing this issue