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bio-small-rna-seq-mirdeep2-analysis

Maintainer FreedomIntelligence · Last updated April 1, 2026

Identify and quantify known/novel miRNAs with miRDeep2.

OpenClawNanoClawAnalysisReproductionbio-small-rna-seq-mirdeep2-analysis🧠 bioos extended suitebioos extended bioinformatics suiteidentify

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-small-rna-seq-mirdeep2-analysis

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • bowtie-build genome.fa genome_index.
  • mapper.pl reads.fastq \ -e \ -h \ -i \ -j \ -k TGGAATTCTCGGGTGCCAAGG \ -l 18 \ -m \ -p genome_index \ -s reads_collapsed.fa \ -t reads_vs_genome.arf \ -v.

Source Doc

Excerpt From SKILL.md

Predict novel miRNAs

miRDeep2.pl
reads_collapsed.fa
genome.fa
reads_vs_genome.arf
mature_ref.fa
mature_other.fa
hairpin_ref.fa
-t Human
2> report.log

Download from miRBase

wget https://www.mirbase.org/download/mature.fa wget https://www.mirbase.org/download/hairpin.fa

Extract species-specific sequences

grep -A1 ">hsa-" mature.fa > mature_human.fa grep -A1 ">hsa-" hairpin.fa > hairpin_human.fa

Use cases

  • Use bio-small-rna-seq-mirdeep2-analysis for genomics and bioinformatics workflows.
  • Apply bio-small-rna-seq-mirdeep2-analysis 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

  • smrna-preprocessing - Prepare reads for miRDeep2
  • mirge3-analysis - Faster quantification alternative
  • differential-mirna - DE analysis of miRNA counts

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