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.
npx skills add majiayu000/claude-skill-registry --skill clip-alignment-gptomics-bioskills --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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
- STAR Alignment
- Bowtie2 Alternative
- Post-Alignment Processing
- Related Skills
STAR --runMode alignReads \ bowtie2 -x genome_index \ Index samtools index aligned.bam Deduplicate with UMIs umi_tools dedup \
What does the bio-clip-seq-clip-alignment skill do?
Align CLIP-seq reads to the genome with crosslink site awareness. Use when mapping preprocessed CLIP reads for peak calling.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill clip-alignment-gptomics-bioskills --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.