bio-ribo-seq-riboseq-preprocessing
Preprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment. Use when preparing Ribo-seq reads for downstream analysis of translation.
npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-ribo-seq-riboseq-preprocessing --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: Bowtie2 2.5.3+, STAR 2.7.11+, cutadapt 4.4+, numpy 1.26+, pysam 0.22+, samtools 1.19+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures - 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. # Ribo-seq Preprocessing **"Preprocess my ribosome profiling data"** → Trim adapters, size-select ribosome-protected fragments (26-34 nt), remove rRNA contamination, and align to the transcriptome for translation analysis. - CLI: `cutadapt` → `bowtie2` (rRNA removal) → `STAR` (genome alignment) ## Workflow Overview ``` Raw Ribo-seq FASTQ | v Adapter trimming (cutadapt) | v Size selection (25-35 nt typical) | v rRNA removal (SortMeRNA/bowtie2) | v Alignment to transcriptome | v Quality filtered BAM ``` ## Adapter Trimming **Goal:** Remove 3' adapter sequences from ribosome footprint reads to recover the true insert. **Approach:** Run cutadapt with the known adapter
- Version Compatibility
- Workflow Overview
- Adapter Trimming
- Size Selection
- rRNA Removal
- Alignment to Transcriptome
- Quality Metrics
- Python Preprocessing
- Related Skills
Trim 3' adapter cutadapt \ input.fastq.gz Select ribosome footprint size range trimmed.fastq.gz Option 1: SortMeRNA (comprehensive) sortmerna \ Option 2: Bowtie2 to rRNA index bowtie2 -x rRNA_index \ STAR alignment (spliced)
What does the bio-ribo-seq-riboseq-preprocessing skill do?
Preprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment. Use when preparing Ribo-seq reads for downstream analysis of translation.
How do I install it?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-ribo-seq-riboseq-preprocessing --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From FreedomIntelligence/OpenClaw-Medical-Skills, a repository with 2,909 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.