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bio-workflows-smrna-pipeline

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

Small RNA-seq: miRNA identification → quantification → DE analysis.

OpenClawNanoClaw分析处理复现实验bio-workflows-smrna-pipeline🧠 bioos extended suitebioos extended bioinformatics suitesmall

原始来源

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-workflows-smrna-pipeline

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

  • cutadapt - TGGAATTCTCGGGTGCCAAGG \ --minimum-length 18 --maximum-length 30 \ -o trimmed.fastq.gz reads.fastq.gz。
  • mapper.pl trimmed.fastq.gz -e -h -i -j -l 18 \ -m -p genome_index -s reads_collapsed.fa \ -t reads_collapsed_vs_genome.arf。

原始文档

SKILL.md 摘录

miRNA quantification and novel prediction

miRDeep2.pl reads_collapsed.fa genome.fa
reads_collapsed_vs_genome.arf
mature_ref.fa none hairpin_ref.fa


## miRanda for target prediction

miranda mature_mirnas.fa target_3utrs.fa -out targets.txt

QC Checkpoints

  1. After trimming: Size distribution should peak at 21-23nt
  2. After alignment: >70% mapping rate expected
  3. After DE: Check volcano plot and PCA

适用场景

  • Use bio-workflows-smrna-pipeline ，用于 genomics 、 bioinformatics workflows。
  • Apply bio-workflows-smrna-pipeline to sequencing，variant，或 omics analysis tasks。

不适用场景

  • Do not rely on this catalog entry alone ，用于 installation 或 maintenance details。

上游相关技能

  • small-rna-seq/mirdeep2-analysis - Detailed miRDeep2
  • small-rna-seq/differential-mirna - DE analysis
  • small-rna-seq/target-prediction - Target analysis

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