Consensus peaks and paired-fragment counts

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These three scripts are concise public-release adaptations. They preserve the sample order, merge rules, fragment-counting options, validation checks, and overwrite protection of the validated workflow, but they were not executed to create a new public result set.

Required environment variables:

export PROJECT_ROOT=/path/to/bulk-atacseq-mature-memory-nk
export INPUT_ROOT=/path/to/validated_bam_bai_and_broadpeak_inputs
export TOOL_DIR=/optional/path/to/analysis/bin
export EXPECTED_HOST=/optional/short_hostname

Run from PROJECT_ROOT, one stage at a time:

ATTEMPT=public_reproduction bash workflow/week2_consensus_counts/01_build_consensus_peaks.sh
ATTEMPT=public_reproduction bash workflow/week2_consensus_counts/02_count_fragments.sh
ATTEMPT=public_reproduction python3 workflow/week2_consensus_counts/03_create_clean_count_matrix.py

The expected input basenames and fixed biological order are defined in config/week2_samples.tsv. The scripts refuse to overwrite an existing attempt.

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