Mixcr Analysis

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, refineTagsA…