AgentSkillsCN

bio-clip-seq-clip-alignment

在考虑交联位点的前提下，将 CLIP-seq 读段比对至基因组。在为峰位识别而对预处理后的 CLIP 读段进行比对时，可选用此功能。

SKILL.md
--- frontmatter
name: bio-clip-seq-clip-alignment
description: Align CLIP-seq reads to the genome with crosslink site awareness. Use when mapping preprocessed CLIP reads for peak calling.
tool_type: cli
primary_tool: STAR

CLIP-seq Alignment

STAR Alignment

bash
STAR --runMode alignReads \
    --genomeDir STAR_index \
    --readFilesIn trimmed.fq.gz \
    --readFilesCommand zcat \
    --outFilterMultimapNmax 1 \
    --outFilterMismatchNmax 1 \
    --alignEndsType EndToEnd \
    --outSAMtype BAM SortedByCoordinate \
    --outFileNamePrefix clip_

Bowtie2 Alternative

bash
bowtie2 -x genome_index \
    -U trimmed.fq.gz \
    --very-sensitive \
    -p 8 \
    | samtools view -bS - \
    | samtools sort -o aligned.bam

Post-Alignment Processing

bash
# Index
samtools index aligned.bam

# Deduplicate with UMIs
umi_tools dedup \
    --stdin=aligned.bam \
    --stdout=deduped.bam

Related Skills

  • •clip-preprocessing - Prepare reads
  • •clip-peak-calling - Call peaks