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10x Genomics
Single Cell Gene Expression

SC_RNA_COUNTER_CSCLOUPE_PREPROCESSSC_RNA_COUNTERCELLRANGER_PREFLIGHTCELLRANGER_PREFLIGHT_LOCALCHEMISTRY_DETECTORDETECT_CHEMISTRYSC_RNA_ANALYZERANALYZER_PREFLIGHTCOMBINE_CLUSTERINGMERGE_CLUSTERSPREPROCESS_MATRIXRUN_DIFFERENTIAL_EXPRESSIONRUN_GRAPH_CLUSTERINGRUN_KMEANSRUN_MULTIGENOME_ANALYSISRUN_PCARUN_TSNESUMMARIZE_ANALYSISSETUP_CHUNKSSUMMARIZE_REPORTS_BASIC_SC_RNA_COUNTERALIGN_READSATTACH_BCS_AND_UMISBUCKET_BY_BCCHUNK_READSCOUNT_GENESEXTRACT_READSFILTER_BARCODESMARK_DUPLICATESREPORT_MOLECULESSORT_BY_BCSORT_BY_POSSUBSAMPLE_READSSUMMARIZE_ATTACHSUMMARIZE_BASIC_REPORTSSUMMARIZE_MKDUPSUMMARIZE_READ_REPORTS
  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.