name: bio-clip-seq-binding-site-annotation
description: 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.
tool_type: mixed
primary_tool: ChIPseeker
measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.
allowed-tools:
- read_file
- run_shell_command
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
By