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mixcr-analysis

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Align V(D)J reads and assemble TCR/BCR clonotypes with MiXCR, driven by a chemistry-matched preset. Use when choosing/auditing the preset for a library (5'RACE/template-switch vs multiplex-primer amplicon -> rigid vs floating boundaries; RNA vs gDNA -> --rna/--dna; bulk vs 10x single-cell; UMI vs no-UMI -> tag pattern and barcode collapse; kit presets Takara/NEBNext/QIAseq/BD/MiLaboratory); assembling clonotypes by CDR3 vs VDJRegion; setting the reads-vs-UMI-vs-cell quantitation denominator; exporting native MiXCR fields vs AIRR rearrangement TSV for downstream Immcantation/scirpy/VDJtools; and running alignment/chain-usage QC. Keywords: MiXCR, analyze, align, refineTagsAndSort, assemblePartial, assemble, assembleCells, exportClones, exportAirr, exportQc, CDR3, V(D)J, clonotype, UMI, cell barcode, 10x VDJ, license.

When to use

• Choosing and auditing MiXCR presets
• Aligning V(D)J reads
• Assembling TCR/BCR clonotypes
• Setting quantitation denominators
• Exporting native MiXCR fields
• Exporting AIRR rearrangement TSV
• Running alignment and chain-usage QC
• Activating MiXCR licenses

When not to use

• Using MiXCR 3.x hand-built pipelines
• Running analysis without an activated license

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