数据与复现生物信息与基因组学FreedomIntelligence/OpenClaw-Medical-Skills数据与复现

bio-ribo-seq-riboseq-preprocessing

维护者 FreedomIntelligence · 最近更新 2026年4月1日

Preprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment. Use when preparing Ribo-seq reads for downstream analysis of translation.

OpenClawNanoClaw分析处理复现实验bio-ribo-seq-riboseq-preprocessing🧬 bioinformatics (gptomics bio-* suite)bioinformatics — differential expression & transcriptomicspreprocess

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-ribo-seq-riboseq-preprocessing

维护者: FreedomIntelligence
许可: MIT
最近更新: 2026年4月1日

技能摘要

来自 SKILL.md 的关键信息

2 min

核心说明

CLI：cutadapt → bowtie2 (rRNA removal) → STAR (genome alignment)。
Preprocess my ribosome profiling data" → Trim adapters，size-select ribosome-protected fragments (26-34 nt)，remove rRNA contamination，、 align to transcriptome ，用于 translation analysis. CLI：cutadapt → bowtie2 (rRNA removal) → STAR (genome alignment)。
cutadapt \ - CTGTAGGCACCATCAAT \ -m 20 \ -M 40 \ -o trimmed.fastq.gz \ input.fastq.gz。

原始文档

SKILL.md 摘录

Adapter Trimming

Goal: Remove 3' adapter sequences from ribosome footprint reads to recover the true insert.

Approach: Run cutadapt with the known adapter sequence and length filters to discard fragments outside the expected footprint range.


## Size Selection

**Goal:** Retain only reads corresponding to ribosome-protected fragments (typically 28-32 nt).

**Approach:** Apply minimum and maximum length filters with cutadapt to select the footprint size range.

```bash

## Typical: 28-32 nt (protected by ribosome)

cutadapt \
    -m 28 \
    -M 32 \
    -o size_selected.fastq.gz \
    trimmed.fastq.gz