# 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. Use when this capability is needed.

- Skill: `tomevault-io/bio-clip-seq-clip-alignment` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds@latest add tomevault-io/bio-clip-seq-clip-alignment`
- Raw SKILL.md: https://api.skillmd.com/api/skills/tomevault-io/bio-clip-seq-clip-alignment/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: tomevault-io (https://skillmd.com/u/tomevault-io)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/tomevault-io/bio-clip-seq-clip-alignment

---


## Version Compatibility

Reference examples tested with: Bowtie2 2.5.3+, STAR 2.7.11+, samtools 1.19+

Before using code patterns, verify installed versions match. If versions differ:
- CLI: `<tool> --version` then `<tool> --help` to confirm flags

If code throws ImportError, AttributeError, or TypeError, introspect the installed
package and adapt the example to match the actual API rather than retrying.

# CLIP-seq Alignment

**"Align my CLIP-seq reads to the genome"** → Map preprocessed CLIP reads with splice-aware alignment and crosslink site extraction for downstream peak calling.
- CLI: `STAR` with CLIP-optimized parameters (no multi-mappers, short reads)
- CLI: `bowtie2` for unspliced protocols

## STAR Alignment

**Goal:** Align CLIP-seq reads to the genome with splice awareness and strict uniqueness filtering.

**Approach:** Run STAR with single-mapping only, low mismatch tolerance, and end-to-end alignment to maximize crosslink site precision.

```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

**Goal:** Index aligned reads and remove PCR duplicates using UMI information.

**Approach:** Index the BAM with samtools and run umi_tools dedup to collapse UMI-duplicate reads.

```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

---
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<!-- tomevault:4.0:skill_md:2026-04-11 -->