Incorrect alignments of adapter sequences to reads

[ManoshiDatta]

Hi Vince, thank you for putting together this software. I think it will be very useful for a lot of people.

I tried Scythe out on a test case, and I found that, for the most part, things behaved as they should. However, there were a number of cases where the alignment seemed to be incorrect. For example:

Here, there's clearly a better alignment than the one that was used. What do you think might cause this? I used the default settings for the prior (p), n, and m.

[Babysri]

parameters incorporated in adapter trimming what can be done for it