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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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Split extracted_features file and run methylation calling #20

Closed vahidAK closed 4 years ago

vahidAK commented 4 years ago

Hi @PengNi , I was wondering if is it possible to split extracted_features file and then performing methylation calling on each file separately?

Thanks, Vahid.

PengNi commented 4 years ago

Hi @vahidAK ,

I'm not sure the reason you want to do so. Is that because the generated extracted_features file too big? The modifications can also be called from the fast5 files directly, which skips the extract_feature step.

Or there is another reason?

Best, Peng

vahidAK commented 4 years ago

Thanks for your response, no I have different machines to run and I want to split the file and separate the job between them to be faster.

PengNi commented 4 years ago

Hi @vahidAK ,

Sorry we didn't consider this case before. We may update deepsignal once we get time for this case.

However, you can split the file manually. The extracted_features file is a text file. Each line in the file is a sample to be tested and is independent to other lines.

Best, Peng

vahidAK commented 4 years ago

Thanks, @PengNi

PengNi commented 4 years ago

see commit 89b58d1.