BioSkills 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/GPTomics/bioSkills

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

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

manifest: clip-seq/clip-alignment/SKILL.md

source content

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.

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

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.

# 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