sjcab_peak2anno

sjcab_peak2anno annotates genomic peaks to genes, genomic features, and chromatin states. It provides the peak2anno and sjcab-peak2anno command line interfaces.

Documentation

Read the full documentation at sjcab-peak2anno.readthedocs.io.

• Installation
• Configuration
• Commands
• Input and output
• Python API
• Changelog

Install

Pip version does not require bedtools; auto uses the Python interval backend. To use native bedtools and create a reviewable script, set SJCAB_PEAK2ANNO_BACKEND=bedtools with bedtools available in PATH. The generated bedtools-peak2anno.sh supports mode 1 (one wide window) and mode 2 (promoter-first, enhancer-second).

pip install sjcab_peak2anno

The conda package does not require external interval tools.

conda install stjudecab::sjcab_peak2anno

Quick start

# it would automatic sjcab_peak2anno_db install hg38 v31 and annotate peaks.bed
wget https://github.com/stjudecab/sjcab_peak2anno/raw/refs/heads/master/tests_data/peaks.bed
peak2anno peak2gene peaks.bed

Command examples

Annotate a BED peak to nearby genes. Omitting -o writes the table to stdout:

peak2anno peak2gene tests_data/peaks.bed \
  --tss-bed tests_data/tss.bed \
  --prom-enha-cutoffs 2000,50k

Example output (tab-delimited):

chr1  50  150  peak1  GeneA  ENSGA  .  .  GeneA  ENSGA  0

Run multiple annotations in one table with the combined command syntax using default hg38 v31:

peak2anno peak2gene narrow2feature tests_data/peaks.bed \
  --workers 2 -o combined.tsv

Representative combined output columns look like this:

chr  start  end  peak  Closest_Gene  FeatureAssignment
chr1 100000 101000 peak1 GeneA        Promoter

Annotate both anchors of a BEDPE loop with loop2gene, loop2feature, or loop2state:

peak2anno loop2gene loops.bedpe --tss-bed annotations/hg38/tss.bed -o loops.tsv

Representative loop output contains separate anchor columns:

chr1 100000 101000 chr1 200000 201000 anchor1_Closest_Gene anchor2_Closest_Gene
chr1 100000 101000 chr1 200000 201000 GeneA                 GeneC