bio-atac-seq-atac-qc

Fragment Size Distribution

Goal: Assess ATAC-seq library quality by visualizing the characteristic nucleosome periodicity in fragment sizes.

Approach: Extract insert sizes from the BAM file using Picard or samtools, producing a distribution that should show NFR (<100 bp) and mono-nucleosome (~200 bp) peaks.

## Using samtools

samtools view -f 66 sample.bam | \
    awk '{print sqrt($9^2)}' | \
    sort | uniq -c | \
    awk '{print $2"\t"$1}' > fragment_sizes.txt

TSS Enrichment Score

Goal: Quantify signal enrichment at transcription start sites as a key ATAC-seq quality metric.

Approach: Create a TSS BED file, compute a signal matrix around TSS positions using deepTools, then plot the enrichment profile.