bio-clip-seq-clip-alignment
SkillDev toolsGives your agent a library of medical AI skills for tasks like biomedical text analysis.
Available today. Use it from your connected AI after setup.
No other account needed.
Connect ahel once, and every AI you use reads what you have installed.
Then ask your AI: use the bio-clip-seq-clip-alignment skill
About this capability
The largest open-source medical AI skills library for OpenClaw🦞.
What this skill tells your AI
The instructions your AI receives, as published by freedomintelligence/openclaw-medical-skills in skills/bio-clip-seq-clip-alignment/SKILL.md and read by ahel’s review.
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 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools:
- read_file
- run_shell_command
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
Signals
- GitHub stars
- 3k
- Forks
- 407
- Last commit
- Jul 2026
Advanced
- Catalog kind
- skill
- Gateway key
bio-clip-seq-clip-alignment- Source
- github.com/freedomintelligence/openclaw-medical-skills