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smrna-pipeline

separate

Orchestrates the end-to-end small RNA-seq pipeline from FASTQ to differential miRNAs and expression-filtered targets, chaining kit-aware cutadapt trimming (adapter on every read, UMI/4N handling), miRge3 known+isomiR quantification or miRDeep2 novel discovery, compositionally-aware DESeq2, and miRanda target prediction. Use when committing the library-kit adapter/UMI handling once, choosing the NORMALIZER (which drives which miRNAs are called DE more than the DE model does), deciding known quantification vs novel discovery, handling biofluid/plasma libraries that lack a trustworthy endogenous normalizer, routing tRF/piRNA reads to their own profiling, or feeding RAW (not RPM) counts with size-factor inspection into DE. Hands mechanism to the small-rna-seq component skills; not a re-teach of any single step.

When to use

• small RNA-seq pipeline from FASTQ to differential miRNAs
• kit-aware cutadapt trimming
• UMI/4N handling
• miRge3 known+isomiR quantification
• miRDeep2 novel discovery
• compositionally-aware DESeq2
• miRanda target prediction
• routing tRF/piRNA reads to profiling

When not to use

• re-teach of any single step
• position-dedup a non-UMI small-RNA library
• using RPM counts for DE

Skill page

Source