Version Compatibility

Reference examples tested with: bedtools 2.31+, samtools 1.19+

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.

bedGraph Handling

"Work with bedGraph signal tracks" → Create, manipulate, and convert bedGraph files for displaying coverage or signal intensity on genome browsers.

• CLI: bedtools genomecov -bg to generate, bedGraphToBigWig to convert
• Python: pyBigWig, pybedtools

bedGraph is a text format for displaying continuous-valued data on genome browsers. Common for coverage, signal intensity, and scores.