Used to filter and bin data generated by the bismark_methylation_extractor when running with the -CX flag. Will also work for binning when run with the CpG only report.
- Python 3
- python CX_filtering.py [-b|--binSize BINSIZE] [-c|--context CONTEXT] [-wx] [-a|--absolute] input.CX_report.txt.gz
- input.CX_report.txt.gz should be the CX report file generated by bismark methylation extractor when run with the -CX flag. This input file must be gzipped.
- The raw CX report generated by bismark will be large and contain mostly 0's. It is highly recommended that you pre-filter this file to, at the very least, remove the locations with no read coverge.
- -h,--help: Display the help message
- -b,--binSize: Specify the bin size data should be collected in - default = 200
- -c,--context: Input the cytosine context to extarct from the data, (CH, CG, CHH, CHG, C) - default = CH
- -wx: output the extracted data to a file, file will be gzipped
- -a,--absolute: Print total values for methylated and unmethylated cytosines, does not calculate percentage