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WGLab / DeepMod

DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications
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Question about the format of input data #16

Closed Musketeer-D closed 5 years ago

Musketeer-D commented 5 years ago

As albacore will output two subfolder in the workspace, one named"fail", another one named "pass", should I put both fail and pass fast5 file into DeepMod to do the methylation analysis? If I should , should I set the "--recursive" of "DeepMod.py detect " to 2 ? as there are two-layer folder.

liuqianhn commented 5 years ago

Hi @DAVID2022 , if you have high coverage data, it would be better to only use those reads from 'pass' folder. I have no evidence to show how 'fail' reads would make the prediction worse or better. But if you want to use both reads from 'fail' and 'pass', you can just set '--recursive 1' not '2' since the program uses the bool value from this parameter.

Musketeer-D commented 5 years ago

thank you very much!