bio-clip-seq-clip-alignment
This Claude Code skill aligns CLIP-seq reads to a reference genome using STAR or Bowtie2, with options for controlling multimapping and mismatch thresholds to preserve crosslink site specificity. Use this skill after preprocessing CLIP-seq reads and before peak calling to generate sorted, indexed BAM files suitable for downstream analysis of RNA-protein interaction sites.
git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills /tmp/bio-clip-seq-clip-alignment && cp -r /tmp/bio-clip-seq-clip-alignment/skills/bio-clip-seq-clip-alignment ~/.claude/skills/bio-clip-seq-clip-alignmentSKILL.md
<!--
# COPYRIGHT NOTICE
# This file is part of the "Universal Biomedical Skills" project.
# Copyright (c) 2026 MD BABU MIA, PhD <md.babu.mia@mssm.edu>
# All Rights Reserved.
#
# This code is proprietary and confidential.
# Unauthorized copying of this file, via any medium is strictly prohibited.
#
# Provenance: Authenticated by MD BABU MIA
-->
---
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
```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
<!-- AUTHOR_SIGNATURE: 9a7f3c2e-MD-BABU-MIA-2026-MSSM-SECURE -->Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements, enzyme activity assays, or protein sequence optimization. Also use for submitting experiments via API, tracking experiment status, downloading results, optimizing protein sequences for better expression using computational tools (NetSolP, SoluProt, SolubleMPNN, ESM), or managing protein design workflows with wet-lab validation.
Time-blind friendly planning, executive function support, and daily structure for ADHD brains. Specializes in realistic time estimation, dopamine-aware task design, and building systems that
This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.
Browse the web for any task — research topics, read articles, interact with web apps, fill forms, take screenshots, extract data, and test web pages. Use whenever a browser would be useful, not just when the user explicitly asks.
AI驱动的综合健康分析系统，整合多维度健康数据、识别异常模式、预测健康风险、提供个性化建议。支持智能问答和AI健康报告生成。
Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.