cangermueller/deepcpg

Negative strand index input

yxwucq opened this issue · 0 comments

Hi:

I'm trying to use the package to deal with my sparse DNA methylation data, then I find the same issue as: #33 #33

I believe the problem is only with the negative strand, because only about half of the data trigger the warning and they are all in the negative strand. I try to suppress the warning by add the conditions in dcpg_data.py and it works.

if seq[p:p + 2] != 'CG' and seq[p-1:p+1] != 'CG': # make the change to suppress the warnings

However, when considering sites from negative strand, it is strange to use the opposite positive strand sequence as input for training, and it makes me confused. I wonder if there is any reason behind it.