Nicolas Dierckxsens

ok, and when you did it before, it also got stuck at Seed retrieval? With a MAF lower than 0.01 that can happen

Hi, Could you send me the seed file?

Did you use the chloroplast assembly as a reference and seed or some online reference?

Because you have a lot of homoplasmies, so your reference is probably not from that dataset? if you run again, please use the extended log (set to 1), then I...

Ah sorry coverage seems enough.., but results are bit weird indeed, if you send me one dataset, I can also try myself if you want

But since all heteroplasmy is found in one short region, I would guess there is no heteroplasmy, something surely went wrong in that area

nicolasdierckxsens at hotmail dot com

How did you filter them? And are the raw files very large?

Can you run it again with extended log option set to 1 and send me that file? Then I can see if it is possible to extend.

Hi, Sorry I was away. That's a big log :) It didn't circularize because you have a long repetitive region, both sides end up in that region, so it seems...