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bioinfomaticsCSU / deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads
GNU General Public License v3.0
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Model training, feature extraction error. #32

Closed vahidAK closed 4 years ago

vahidAK commented 4 years ago

Hi @PengNi ,

I am trying to use DeepSignal to train a model. I found the zero-based position of CpGs that are modified or not. Then I used these position files to extract features to train a model on. But, when I used the extract module it does not extract any features?

Here is my command: deepsignal extract -i fast5s/ --reference_path hg38.fa --methy_label 1 --positions position.tsv -o extracted_featur.tsv

and here is the header of my position file: 1 3287543 1 3287547 1 3287551 1 3287555 1 3287559 1 3287563 1 3287567 1 3287571 1 3287575 1 3287579

My position file does not have a header.

However, when I do not give the position option to the command it extracts the features.

Thanks, Vahid.

PengNi commented 4 years ago

Hi @vahidAK ,

The position file must be in the format of 1 3287543 + or 1 3287543 -, with a third column (+/-) indicates the strand of the position (in forward or backward strand). And the delimiter is \t.

Best, Peng