Claude-skill-registry bio-clip-seq-clip-alignment

Align CLIP-seq reads to the genome with crosslink site awareness. Use when mapping preprocessed CLIP reads for peak calling.

install

source · Clone the upstream repo

git clone https://github.com/majiayu000/claude-skill-registry

Claude Code · Install into ~/.claude/skills/

T=$(mktemp -d) && git clone --depth=1 https://github.com/majiayu000/claude-skill-registry "$T" && mkdir -p ~/.claude/skills && cp -r "$T/skills/data/clip-alignment" ~/.claude/skills/majiayu000-claude-skill-registry-bio-clip-seq-clip-alignment && rm -rf "$T"

manifest: skills/data/clip-alignment/SKILL.md

CLIP-seq Alignment

STAR Alignment

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

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

Post-Alignment Processing

# 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