atac-seq-bam-read-alignment-processing

atac-seq-bam-read-alignment-processing

Summary

Extract and aggregate Tn5 insertion positions from aligned ATAC-seq BAM files within fixed-width windows around genomic features (e.g., transcription factor binding motifs) to enable footprint detection and chromatin accessibility analysis. This processing step bridges raw sequencing alignments to footprinting signal by computing positional distributions of insertion events.

When to use

When you have aligned ATAC-seq BAM files and need to quantify Tn5 transposase insertion patterns around specific genomic coordinates (motif sites, peaks, regulatory regions) to detect transcription factor occupancy footprints or compare chromatin accessibility between bound and unbound sites. Apply this skill after read alignment but before footprint scoring or differential binding analysis.

When NOT to use

• Input BAM file is not properly coordinate-sorted or lacks proper pair information—preprocessing alignment files is a prerequisite, not a use of this skill.
• Target coordinates are undefined or lack biological annotation; this skill requires specific genomic intervals (motifs, peaks, etc.), not unstructured genomic regions.
• The analysis goal is to detect novel accessible regions genome-wide rather than footprinting at known or predicted binding sites; use peak calling instead.

Inputs

• Aligned ATAC-seq BAM file (coordinate-sorted, with read pairs)
• Genomic coordinates in BED format (transcription factor motif sites, peaks, or other regulatory regions)
• Classification/annotation of sites as bound or unbound (thresholded by accessibility signal or binding confidence)

Outputs

• Insertion count matrix (positions × site class)
• Positional distribution statistics (mean, standard deviation per position per class)
• Aggregate insertion profile plot or heatmap visualization showing footprint depletion at bound sites
• Corrected or raw insertion bigWig files (optional, for downstream visualization)

How to apply