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smrna-preprocessing

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Trims kit-specific 3' adapters, strips UMIs or 4N degenerate ends, size-selects, and collapses small RNA-seq reads (miRNA, piRNA, tRF) with cutadapt or fastp. Use when choosing the kit's 3' adapter; setting the size window (18-26 nt miRNA vs 24-32 nt piRNA); deciding whether a library carries a true UMI (QIAseq) versus a 4N debiasing spacer (NEXTflex); reading the read-length histogram to judge library quality; or deciding whether to collapse identical reads before mapping.

When to use

• choosing the kit's 3' adapter
• setting the size window (18-26 nt miRNA vs 24-32 nt piRNA)
• deciding whether a library carries a true UMI (QIAseq) versus a 4N debiasing spacer (NEXTflex)
• reading the read-length histogram to judge library quality
• deciding whether to collapse identical reads before mapping
• removing the 3' adapter
• removing any UMI or 4N degenerate bases
• collapsing identical reads to a counted FASTA

When not to use

• fixing ligation bias
• quantification or discovery

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