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Bio Clip Seq Binding Site Annotation

Annotate CLIP-seq binding sites to genomic features including 3'UTR, 5'UTR, CDS, introns, and ncRNAs. Use when characterizing where an RBP binds in transcripts.

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Binding Site Annotation

Using ChIPseeker (R)

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

tools-only/X-Skills/tree/main/development/tools/1178-name-skill_3eeda5cd commit 4417c0a7ca

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npx skillmds add tools-only/bio-clip-seq-binding-site-annotation-2