Fast5 Files must be basecalled with methylation-aware model
ModExtract -- Extract FastQ and Modification Results from Fast5 File
Usage:
extract_mod.py INPUTDIR
extract_mod.py [options] INPUTDIR
Options:
-h --help Show this screen
-t --threads=N Use N threads [default: 4]
-o DIR --outDir=DIR Output directory [default: InputDirectory]
-a STR --analysis=STR Select specific basecalling analysis to extracat [default: latest]
-q --noFastq Dont extract fastQ files
-k --keepSkipped Include Fast5 from the Skipped folder
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Clone repository
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Install python requirements (or make venv)
pip3 install -r requirements.txt
This script produces:
Gzip
compressed FastQs- Modification informations. The files are gzipped and pickled python libraries. To load the data into python for further analysis use the following code:
import pickle
import gzip
dat = pickle.load(gzip.open("myread.mod.gz", "rb"))
This data is pretty useless on its own, a consensus module based on a minimap alignment might be really useful...