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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---
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
---
# Binding Site Annotation
## Using ChIPseeker (R)
```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
```bash
# Annotate to UTRs
bedtools intersect -a peaks.bed -b 3utr.bed -wa -wb > peaks_3utr.bed
```
## Python Annotation
```python
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
