search

iprada / Circle-Map

A method for circular DNA detection based on probabilistic mapping of ultrashort reads
MIT License
62 stars 19 forks source link

A problem of searching principle of Circle-Map #97

Open FeiLiuEM opened 11 months ago

FeiLiuEM commented 11 months ago

Circle-Map is a very good algorithm and help me much.

I have a problem of searching principle:

Is it possible that the predicted eccDNA includes more than one eccDNA?

In other words, after recognizing split records, is it possible for the algorithm to recognize adjacent eccDNA as one eccDNA?

Thanks！

iprada commented 11 months ago

ey FeiLiuEM,

Thanks for you kind words. I appreciate :)

Circle-Map clusters split reads intervals (i.e. eccDNAs) that reciprocally overlap by 0.95 percent. Therefore, if there are nested structures it should capture them (circles inside other circles)

best,

Iñigo

FeiLiuEM commented 11 months ago

Hi Iñigo,

Thank you very much for your answer！

It addresses an important underlying problem in our study.

All the best,

Fei Liu

iprada commented 11 months ago

Glad to hear.

Happy circle hunting!

Iñigo