HOME  ›   pipelines

10x Genomics
Single Cell Immune Profiling

Cell Ranger , printed on 04/13/2025

SC_VDJ_ASSEMBLER_CSCOPY_VDJ_REFERENCESC_MULTI_CSEMPTY_IF_NULLFULL_COUNT_INPUTSEXPAND_SAMPLE_DEFFULL_VDJ_INPUTSMAKE_BASIC_CONFIGSC_MULTI_CORECOUNT_ANALYZERSC_RNA_ANALYZERANALYZER_PREFLIGHTCHOOSE_DIMENSION_REDUCTIONCHOOSE_DIMENSION_REDUCTION_OUTPUTCOMBINE_CLUSTERINGCORRECT_CHEMISTRY_BATCHMERGE_CLUSTERSPREPROCESS_MATRIXRUN_DIFFERENTIAL_EXPRESSIONRUN_FBPCARUN_GRAPH_CLUSTERINGRUN_KMEANSRUN_MULTIGENOME_ANALYSISRUN_PCARUN_TSNERUN_UMAPSUMMARIZE_ANALYSIS_CRISPR_ANALYZERCALL_PROTOSPACERSSUMMARIZE_CRISPR_ANALYSIS_PERTURBATIONS_BY_FEATURE_PERTURBATIONS_BY_TARGETDETECT_COUNT_CHEMISTRYDISABLE_FEATURE_STAGESMAKE_FULL_CONFIGMULTI_GEM_WELL_PROCESSORCOUNT_GEM_WELL_PROCESSORCHECK_BARCODES_COMPATIBILITYMULTI_SETUP_CHUNKSPARSE_TARGET_FEATURES_BASIC_SC_RNA_COUNTERFILTER_BARCODES_CELLS_REPORTERSUBSAMPLE_READSSUMMARIZE_BASIC_REPORTSWRITE_MOLECULE_INFO_MATRIX_COMPUTERALIGN_AND_COUNTBARCODE_CORRECTIONCOLLATE_METRICSMAKE_SHARDMERGE_METRICSWRITE_BARCODE_SUMMARYWRITE_H5_MATRIXWRITE_MATRIX_MARKETWRITE_POS_BAM_SLFE_PARTIAL_FIRST_PASSINITIAL_ALIGN_AND_COUNTSET_TARGETED_UMI_FILTERSUBSAMPLE_BARCODES_TARGETED_ANALYZERCALCULATE_TARGETED_METRICSSUBSAMPLE_OFF_TARGET_READSSUBSAMPLE_ON_TARGET_READSSUMMARIZE_TARGETED_ANALYSISVDJ_B_GEM_WELL_PROCESSORMULTI_SETUP_CHUNKSSC_VDJ_CONTIG_ASSEMBLERASSEMBLE_VDJBARCODE_CORRECTIONMAKE_SHARDRUST_BRIDGEVDJ_T_GEM_WELL_PROCESSORMULTI_SETUP_CHUNKSSC_VDJ_CONTIG_ASSEMBLERASSEMBLE_VDJBARCODE_CORRECTIONMAKE_SHARDRUST_BRIDGEMULTI_REPORTERCLOUPE_PREPROCESSSUMMARIZE_REPORTSVDJ_B_REPORTERREPORT_CONTIGSSUMMARIZE_VDJ_REPORTSVLOUPE_PREPROCESSVDJ_T_REPORTERREPORT_CONTIGSSUMMARIZE_VDJ_REPORTSVLOUPE_PREPROCESSSPLIT_VDJ_INPUTSVDJ_B_CLONOTYPE_ASSIGNERASSEMBLE_CONSENSUSCREATE_AIRR_TSVGROUP_CLONOTYPESVDJ_CHEMISTRY_DETECTORDETECT_CHEMISTRYDETECT_VDJ_RECEPTORVDJ_T_CLONOTYPE_ASSIGNERASSEMBLE_CONSENSUSCREATE_AIRR_TSVGROUP_CLONOTYPESVDJ_PREFLIGHTVDJ_PREFLIGHT_LOCAL
←  SC_VDJ_ASSEMBLER_CS

This is the main Cell Ranger V(D)J pipeline that assembles and annotates single-cell V(D)J transcript sequences. This outer wrapper pipeline prepares files for final output.