AgentSkillsCN

bio-clip-seq-binding-site-annotation

将 CLIP-seq 结合位点注释至基因组特征，包括 3'UTR、5'UTR、CDS、内含子以及非编码 RNA。在表征 RBP 在转录本中的结合位点时，可选用此功能。

SKILL.md
--- frontmatter
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