Version Compatibility

Reference examples tested with: bedtools 2.31+, deepTools 3.5+, numpy 1.26+, pandas 2.2+, picard 3.1+, pyBigWig 0.3+, pysam 0.22+, samtools 1.19+

Before using code patterns, verify installed versions match. If versions differ:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

ATAC-seq Quality Control

"Check the quality of my ATAC-seq library" → Evaluate fragment size distribution (nucleosome periodicity), TSS enrichment, FRiP, and library complexity to assess chromatin accessibility experiment quality.

• CLI: deeptools bamPEFragmentSize, picard CollectInsertSizeMetrics
• Python: pysam for custom fragment analysis

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 Picard
java -jar picard.jar CollectInsertSizeMetrics \
    I=sample.bam \
    O=insert_sizes.txt \
    H=insert_sizes.pdf \
    M=0.5

# 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.