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10x Genomics
Single Cell Gene Expression

SC_RNA_COUNTER_CSSC_RNA_COUNTERALIGN_READSATTACH_BCS_AND_UMISCELLRANGER_PREFLIGHTCELLRANGER_PREFLIGHT_LOCALCOUNT_GENESEXTRACT_READSFILTER_BARCODESMARK_DUPLICATESREPORT_MOLECULESSC_RNA_ANALYZERANALYZER_PREFLIGHTRUN_DIFFERENTIAL_EXPRESSIONRUN_KMEANSRUN_MULTIGENOME_ANALYSISRUN_PCARUN_PREPROCESSRUN_TSNESUMMARIZE_ANALYSISSETUP_CHUNKSSORT_BY_POSSORT_BY_QNAMESUBSAMPLE_READSSUMMARIZE_REPORTS_BCSORTERBUCKET_BY_BCSORT_BY_BC
  SC_RNA_COUNTER_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.