bio-methylation-callinglisted

## Version Compatibility Reference examples tested with: pandas 2.2+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - CLI: `<tool> --version` then `<tool> --help` to confirm flags If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Methylation Calling **"Extract methylation calls from my Bismark BAM"** → Generate per-cytosine methylation reports (CpG, CHG, CHH contexts) from aligned bisulfite sequencing data. - CLI: `bismark_methylation_extractor --bedGraph --cytosine_report sample.bam` ## Basic Extraction ```bash # Extract methylation calls from Bismark BAM bismark_methylation_extractor --gzip --bedGraph \ sample_bismark_bt2.bam ``` ## Paired-End Extraction ```bash bismark_methylation_extractor --paired-end --gzip --bedGraph \ sample_bismark_bt2_pe.bam ``` ## Common Options ```bash bismark_methylation_extractor \ --paired-end \ # For paired-end data --gzip \ # Compress output --bedGraph \ # Generate bedGraph file --cytosine_report \ # Genome-wide cytosine report --genome_folder /path/to/genome/ \ # Required for cytosine_report --buffer_size 10G \ # Memory buffer --parallel 4 \ # Parallel extraction -o output_dir/