end-to-end-bioinformatics-pipeline-testing

end-to-end-bioinformatics-pipeline-testing

Summary

Verify that a cloned bioinformatics tool (shell and R scripts) executes correctly from start to finish on real or representative input data, producing valid output with correct structure and coordinate ranges. This skill validates both tool availability and computational correctness before integration into larger analyses.

When to use

After cloning or installing a peak-calling or genomic analysis tool from a repository, before using it on production data. Triggers include: (1) first deployment of the tool in a new environment, (2) version upgrade or bug-fix release, (3) uncertainty about whether dependencies (R, Bedtools) are correctly installed in your PATH, or (4) need to confirm the tool accepts your input bedgraph format and produces the expected BED region output.

When NOT to use

• Input bedgraph file contains individual reads rather than read-pair density; convert to fragment-level bedgraph first using bedtools genomecov on paired-end BED files.
• Required dependencies (R, Bedtools) are not installed or not in PATH; install and configure them before running end-to-end test.
• Input bedgraph includes zero-signal regions; SEACR expects bedgraph files that omit regions with 0 signal, so preprocess to remove them.

Inputs

• Paired-end CUT&RUN bedgraph file in UCSC bedgraph format (omitting zero-signal regions)
• Control (IgG) bedgraph file or numeric threshold between 0 and 1
• Cloned or installed SEACR repository with shell and R scripts

Outputs

• BED file of enriched regions (.stringent.bed or .relaxed.bed)
• Six-column BED with fields: chromosome, start, end, total signal, max signal, max signal region

How to apply

Clone the tool repository and verify that executable shell and R scripts are present with correct permissions. Prepare a minimal test bedgraph file in UCSC bedgraph format (omitting zero-signal regions) that represents paired-end CUT&RUN sequencing density. Execute the pipeline end-to-end using both required input modes: (a) with a control bedgraph and normalization flag ('norm' or 'non'), and (b) optionally with a numeric threshold (0–1 range) to select top fraction of peaks by signal. Verify the output BED file is produced at the specified prefix, contains valid genomic coordinates (chr, start, end), and includes the six expected fields (chromosome, start, end, total signal, max signal, max signal region). Check that region coordinates are non-negative, start ≤ end, and signal values are numeric and reasonable for your peak height expectations.