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10x Genomics
Single Cell Multiome ATAC + Gene Exp.

Cell Ranger ARC , printed on 04/15/2025

SC_ATAC_GEX_COUNTER_CSARC_COUNTER_PREFLIGHT_LOCALSC_ATAC_GEX_COUNTERARC_COUNTER_PREFLIGHTATAC_GEX_CLOUPE_PREPROCESSCHECK_JOINT_BARCODES_COMPATIBILITYCOMPILE_GEX_BARCODE_METRICSCREATE_JOINT_WEBSUMMARYGEX_SUMMARIZE_REPORTSMERGE_RNA_ATAC_DATASPLIT_SAMPLE_DEFWRITE_POS_BAM_ATAC_MATRIX_COMPUTERALIGN_ATAC_READSGENERATE_PEAK_MATRIXMAKE_ATAC_SHARDSMARK_ATAC_DUPLICATESWRITE_ATAC_BAM_PEAK_CALLERCONVERT_SIGNAL_TRACKCOUNT_CUT_SITESDETECT_PEAKS_FASTQ_STAGERATAC_SETUP_CHUNKSGEX_SETUP_CHUNKS_GEX_CELLS_REPORTERSUBSAMPLE_READSSUMMARIZE_BASIC_REPORTSWRITE_MOLECULE_INFO_GEX_MATRIX_COMPUTERALIGN_AND_COUNTBARCODE_CORRECTIONCOLLATE_METRICSMAKE_READ_SHARDS_STRUCTMAKE_SHARDMERGE_METRICSSET_ALIGNER_SUBSAMPLE_RATEWRITE_BARCODE_INDEXWRITE_BARCODE_SUMMARYWRITE_H5_MATRIXWRITE_MATRIX_MARKET_SLFE_PARTIAL_FIRST_PASS_JOINT_CELL_DETECTORDETECT_JOINT_CELL_BARCODESFILTER_PEAK_MATRIXFILTER_UMI_MATRIXGENERATE_SC_ATAC_COUNTSMERGE_ATAC_RNA_MATRICESMERGE_CELL_METRICSMERGE_EXCLUDED_BARCODESREMOVE_BARCODE_MULTIPLETSREMOVE_GEL_BEAD_DOUBLET_BARCODESREMOVE_LOW_TARGETING_BARCODES_SC_ATAC_GEX_ANALYZERATAC_GEX_SUMMARIZE_ANALYSISPARSE_REDUCED_DIM_ATAC_CLUSTERING_COMPUTERATAC_RUN_GRAPH_CLUSTERINGCLUSTER_CELLSCOMBINE_CLUSTERINGCOMPUTE_DIFFERENTIAL_ATACCOMPUTE_DIFFERENTIAL_GEX_DIMENSION_REDUCER_ATAC_DIMENSION_REDUCERREDUCE_DIMENSIONSRUN_MANIFOLD_PROJECTION_GEX_DIMENSION_REDUCERREDUCE_DIMENSIONSRUN_MANIFOLD_PROJECTION_FEATURE_LINKAGE_COMPUTERCOMPUTE_FEATURE_LINKAGESPREPROCESS_JOINT_MATRIX_GEX_CLUSTERING_COMPUTERATAC_RUN_GRAPH_CLUSTERINGCLUSTER_CELLSCOMBINE_CLUSTERINGCOMPUTE_DIFFERENTIAL_ATACCOMPUTE_DIFFERENTIAL_GEX_PEAK_ANNOTATORANNOTATE_PEAKSCOMPUTE_GC_DISTRIBUTIONGENERATE_TF_MATRIXSCAN_MOTIFS_SC_ATAC_METRIC_COLLECTORCOMPUTE_FRAGMENT_METRICSESTIMATE_LIBRARY_COMPLEXITYMERGE_SINGLECELL_METRICSREPORT_INSERT_SIZESREPORT_TSS_CTCFSUMMARIZE_SINGLECELL_METRICS_SC_ATAC_REPORTERCREATE_WEBSUMMARYSUMMARIZE_REPORTS_SINGLECELL
←  SC_ATAC_GEX_COUNTER_CS

This is an outer wrapper pipeline to check that the input arguments are valid before invoking the main Cell Ranger ARC analysis pipeline. This outer wrapper pipeline prepares files for final output.