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10x Genomics
Single Cell Gene Expression

CELLRANGER_CSCELLRANGERALIGN_READSANALYZE_MATRICESATTACH_BCS_AND_UMISCELLRANGER_PREFLIGHTCELLRANGER_PREFLIGHT_LOCALCOUNT_GENESEXTRACT_UMIFILTER_BARCODESMARK_DUPLICATESREPORT_MOLECULESSETUP_CHUNKSSORT_BY_POSSUMMARIZE_REPORTS_BCSORTERBUCKET_BY_BCSORT_BY_BC
  CELLRANGER_CS

This is the main Cell Ranger pipeline that performs alignment, de-duplication and filtering, and generates gene-cell matrices and gene expression analysis. This outer wrapper pipeline prepares files for final output.