What problem does it solve? Setting up CellRanger multi demultiplexing requires precisely formatted Sample2Barcode CSV files whose column names, quoting conventions, and reference files differ across OCM, HTO/CMO, and Flex v2 multiplexing methods. This Skill eliminates misconfiguration errors by generating the exact FGCZ/SUSHI-specific file formats and parameters for each multiplexing chemistry. ## Core Features & Use Cases - OCM demultiplexing files: Create unquoted CSVs with ocm_barcode_ids columns for On-Chip Multiplexing with OB1-OB4 barcodes (4-plex max, CellRanger 9.0+). - HTO/CMO demultiplexing files: Create quoted CSVs with cmo_ids columns for TotalSeq-B/C hashtag antibodies, including pipe-separated double-hashing support. - Flex v2 probe barcode files: Create CSVs with probe_barcode_ids and description columns for Fixed RNA Panel v2 multiplexing from 4-plex to 384-plex (CellRanger 10.0+). - SUSHI integration guidance: Provides required CellRangerMulti app parameters, MultiplexBarcodeSet reference file selection, gstore folder placement, and troubleshooting for common ezRun errors. - Use Case: A lab delivers 8 pooled samples labeled with TotalSeq-B hashtags B0303-B0305. Use this Skill to generate one {PoolName}_Sample2Barcode.csv per pool, copy them to /srv/gstore/projects/pXXXXX/oXXXXX_metaData/, and configure SUSHI with MultiplexingType = antibody. ## Quick Start Ask the agent to generate a Sample2Barcode file for your pool by providing the sample names and their hashtag, OCM, or Flex v2 probe barcode assignments.
