Skip to content

usage-guide.md

Latest commit

 

History

History
89 lines (70 loc) · 3.23 KB

usage-guide.md

File metadata and controls

89 lines (70 loc) · 3.23 KB

Proximity Operations - Usage Guide

Overview

Proximity operations help you find relationships between genomic features based on their distance. This skill covers finding nearest features (closest), searching within distance windows (window), and extending intervals (slop, flank).

Prerequisites

# bedtools (required)
conda install -c bioconda bedtools

# pybedtools (optional, for Python)
pip install pybedtools

# samtools (for creating genome file from FASTA)
conda install -c bioconda samtools

Quick Start

Tell your AI agent what you want to do:

  • "Find the nearest gene to each of my ChIP-seq peaks"
  • "Get all peaks within 10kb of a TSS"
  • "Create promoter regions 2kb upstream of each gene"

Example Prompts

Finding Nearest Features

"Find the nearest gene to each peak in my ChIP-seq data" "Assign each enhancer to its closest TSS" "Report the distance from each variant to the nearest exon"

Distance-Based Filtering

"Get all peaks within 5kb of any promoter" "Find variants that are within 1kb of a splice site" "Filter enhancers to keep only those within 100kb of a gene"

Extending Intervals

"Extend my peak summits by 250bp on each side" "Create 2kb promoter regions upstream of each TSS" "Get 500bp flanking regions on both sides of my peaks"

Enhancer-Gene Pairing

"Pair each enhancer with genes within 100kb" "Create enhancer-promoter pairs based on proximity"

What the Agent Will Do

  1. Prepare genome file if needed (chromosome sizes)
  2. Extract or create reference features (e.g., TSS from genes)
  3. Run appropriate proximity operation (closest, window, slop)
  4. Filter results by distance if requested
  5. Output paired features with distances

Choosing the Right Operation

Goal Operation Example
Find nearest feature closest Assign peaks to genes
Features within distance window Peaks within 10kb of TSS
Extend interval borders slop Expand peaks by 100bp
Get flanking regions flank Get regions beside features
Move intervals shift Shift by fixed distance

Tips

  • Most operations require a genome file (chromosome sizes); create with cut -f1,2 reference.fa.fai > genome.txt
  • Use -s flag with slop/flank to respect strand direction
  • The closest operation returns "." when no feature exists on the same chromosome
  • Use -d flag with closest to report distances
  • For window operations, use -w for symmetric windows or -l/-r for asymmetric

Resources