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10x Genomics
Single Cell Multiome ATAC + Gene Exp.

SC_ATAC_GEX_COUNTER_CSARC_COUNTER_PREFLIGHT_LOCALSC_ATAC_GEX_COUNTERARC_COUNTER_PREFLIGHTATAC_GEX_CLOUPE_PREPROCESSCOMPILE_GEX_BARCODE_METRICSCREATE_JOINT_WEBSUMMARYGEX_SUMMARIZE_REPORTSMERGE_RNA_ATAC_DATASPLIT_SAMPLE_DEF_ATAC_MATRIX_COMPUTERGENERATE_PEAK_MATRIX_ALIGNERATAC_ALIGN_READSTRIM_READS_PEAK_CALLERCONVERT_SIGNAL_TRACKCOUNT_CUT_SITESDETECT_PEAKS_SORT_AND_MARK_DUPSATAC_MARK_DUPLICATESATTACH_BCSSORT_READS_BY_POS_FASTQ_STAGERCHECK_JOINT_BARCODES_COMPATIBILITYGEX_SETUP_CHUNKS_ATAC_FASTQ_STAGERATAC_DETECT_CHEMISTRYATAC_SETUP_CHUNKS_GEX_CELLS_REPORTERSUBSAMPLE_READSSUMMARIZE_BASIC_REPORTSWRITE_MOLECULE_INFO_GEX_MATRIX_COMPUTERALIGN_AND_COUNTBARCODE_CORRECTIONCOLLATE_METRICSMAKE_SHARDMERGE_METRICSWRITE_BARCODE_SUMMARYWRITE_H5_MATRIXWRITE_MATRIX_MARKETWRITE_POS_BAM_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_ANALYSIS_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_COLLECTORESTIMATE_LIBRARY_COMPLEXITYGENERATE_SEQUENCING_METRICSGENERATE_SINGLECELL_TARGETINGMERGE_SINGLECELL_METRICSREPORT_INSERT_SIZESREPORT_TSS_CTCF_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.