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bio-workflows-smrna-pipeline

Maintainer FreedomIntelligence · Last updated April 1, 2026

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

OpenClawNanoClawAnalysisReproductionbio-workflows-smrna-pipeline🧠 bioos extended suitebioos extended bioinformatics suitesmall

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

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

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • cutadapt -a 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.

Source Doc

Excerpt From SKILL.md

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

Use cases

  • Use bio-workflows-smrna-pipeline for genomics and bioinformatics workflows.
  • Apply bio-workflows-smrna-pipeline to sequencing, variant, or omics analysis tasks.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • 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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