search

PengNi / deepsignal2

GNU General Public License v3.0
27 stars 4 forks source link

question about 'deepsignal2 call_mods ' commands #8

Closed Flower9618 closed 3 years ago

Flower9618 commented 3 years ago

Hi,

I am confused about the argument '--methy_label' in the 'deepsignal2 call_mods' command. If I have one dataset that includes both the methylated and unmethylated class, how should I set the argument '--methy_label'? Thank you very much!

Best, Rong

PengNi commented 3 years ago

Hi @Flower9618 , sorry for the confusion. --methy_label is only designed for training. When using call_mods module, this argument is not used. So it doesn't matter what number you set.

Best, Peng

Flower9618 commented 3 years ago

Hi @Flower9618 , sorry for the confusion. --methy_label is only designed for training. When using call_mods module, this argument is not used. So it doesn't matter what number you set.

Best, Peng

Thank you very much for your prompt reply. So, When I use 'deepsignal2 call_mods' command, it will just use the trained model to call methylation, '--methy_Label' is not used. But in the 'deepsignal2 extract' command， the argument '--methy_label' is used. Is I correct?

PengNi commented 3 years ago

@Flower9618, yes, this is correct.