Version Compatibility

Reference examples tested with: bedtools 2.31+, pandas 2.2+

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.

Binding Site Annotation

"Annotate where my RBP binds in transcripts" → Map CLIP-seq peaks to genomic features (3'UTR, 5'UTR, CDS, introns, ncRNAs) to characterize RNA-binding protein target regions.

• R: ChIPseeker::annotatePeak() with transcript annotation databases
• CLI: bedtools intersect with gene model BED files

Using ChIPseeker (R)

Goal: Classify CLIP-seq binding sites by genomic feature (3'UTR, 5'UTR, CDS, intron).

Approach: Load peaks and a TxDb transcript database, annotate with annotatePeak, and visualize the feature distribution with a pie chart.

library(ChIPseeker)
library(TxDb.Hsapiens.UCSC.hg38.knownGene)

txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene

peaks <- readPeakFile('peaks.bed')
anno <- annotatePeak(peaks, TxDb = txdb)

plotAnnoPie(anno)

Using BEDTools

# Annotate to UTRs
bedtools intersect -a peaks.bed -b 3utr.bed -wa -wb > peaks_3utr.bed

Python Annotation

import pandas as pd

def annotate_peaks(peaks_bed, annotation_gtf):
    '''Annotate peaks to genomic features'''
    # Load peaks and annotations
    # Intersect and categorize
    pass

Related Skills

• clip-peak-calling - Get peaks
• genome-intervals/interval-arithmetic - Intersect peaks with genomic features