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10x Genomics
Single Cell Gene Expression

SC_RNA_AGGREGATOR_CSBUILD_COMBINED_WEB_SUMMARYCOUNT_AGGRCHECK_INVARIANTSCHECK_MOLECULE_INFO_VERSIONCLOUPE_PREPROCESSSC_RNA_AGGREGATORAGGREGATOR_PREFLIGHTMERGE_MOLECULESNORMALIZE_DEPTHSC_RNA_ANALYZERANALYZER_PREFLIGHTCHOOSE_DIMENSION_REDUCTIONCHOOSE_DIMENSION_REDUCTION_OUTPUTCOMBINE_CLUSTERINGCORRECT_CHEMISTRY_BATCHMERGE_CLUSTERSPREPROCESS_MATRIXRUN_DIFFERENTIAL_EXPRESSIONRUN_FBPCARUN_GRAPH_CLUSTERINGRUN_KMEANSRUN_MULTIGENOME_ANALYSISRUN_PCARUN_TSNERUN_UMAPSUMMARIZE_ANALYSISSETUP_SAMPLESSUMMARIZE_AGGREGATED_REPORTSWRITE_MATRICESPARSE_AGGR_CSVVDJ_AGGRCOPY_VDJ_REFERENCEMATCH_VDJ_AGGR_OUTSSC_VDJ_AGGREGATORBUILD_AGGR_WEB_SUMMARYCALCULATE_CLONOTYPE_DIVERSITYFILL_CLONOTYPE_INFOPROCESS_VDJ_PROTORUN_ENCLONE_AGGRSETUP_VDJ_AGGRVLOUPE_PREPROCESSWRITE_AGGR_ANNWRITE_ANN_CSVWRITE_CLONOTYPE_OUTSWRITE_CONSENSUS_TXTWRITE_WEB_SUMMARY_JSON
  SC_RNA_AGGREGATOR_CS

This is the main Cell Ranger pipeline that performs multiple GEM groups aggregation and generates feature-barcode matrices and gene expression analysis. This outer wrapper pipeline prepares files for final output.