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10x Genomics
Single Cell Gene Expression

SC_RNA_COUNTER_CSCLOUPE_PREPROCESSEXPAND_SAMPLE_DEFSC_RNA_COUNTERCHECK_BARCODES_COMPATIBILITYCHEMISTRY_DETECTORDETECT_CHEMISTRYDISABLE_FEATURE_STAGESSC_RNA_ANALYZERANALYZER_PREFLIGHTCHOOSE_DIMENSION_REDUCTIONCHOOSE_DIMENSION_REDUCTION_OUTPUTCOMBINE_CLUSTERINGCORRECT_CHEMISTRY_BATCHMERGE_CLUSTERSPREPROCESS_MATRIXRUN_DIFFERENTIAL_EXPRESSIONRUN_FBPCARUN_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_BASIC_REPORTSSUMMARIZE_READ_REPORTS_CRISPR_ANALYZERCALL_PROTOSPACERSSUMMARIZE_CRISPR_ANALYSIS_PERTURBATIONS_BY_FEATURE_PERTURBATIONS_BY_TARGET
  SC_RNA_COUNTER_CS

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