Version Compatibility

Reference examples tested with: TOBIAS 0.16+, RGT HINT-ATAC 1.0.2+, Wellington (pyDNase) 0.3+, scprinter 0.1+, samtools 1.19+, bedtools 2.31+, pyBigWig 0.3+, MEME suite 5.5+.

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 unexpected errors, introspect the installed package and adapt rather than retrying.

TF Footprinting

"Identify TF binding footprints in my ATAC-seq data" -> Detect short DNA stretches (typically 6-20 bp) of reduced Tn5 cleavage within accessible regions, where a bound TF physically protects DNA. Requires (1) Tn5 sequence-bias correction, (2) per-base footprint scoring, (3) motif-anchored detection.

• CLI: TOBIAS ATACorrect -> TOBIAS ScoreBigwig (formerly FootprintScores) -> TOBIAS BINDetect
• CLI: rgt-hint footprinting --atac-seq (HINT-ATAC, single-step)
• CLI: wellington_footprints.py (legacy DNase, adapted for ATAC)
• Python: scprinter (multi-scale, single-cell aware; Hu 2025 Nature)