# 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.

- Author: mdbabumiamssm
- Repository: mdbabumiamssm/Universal-Life-Science-and-Clinical-Skills-
- Version: 20260206103107
- Stars: 0
- Forks: 0
- Last Updated: 2026-02-06
- Source: https://github.com/mdbabumiamssm/Universal-Life-Science-and-Clinical-Skills-
- Web: https://mule.run/skillshub/@@mdbabumiamssm/Universal-Life-Science-and-Clinical-Skills-~bio-clip-seq-clip-alignment:20260206103107

---

---
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