HOME  ›   pipelines

10x Genomics
Single Cell ATAC

Cell Ranger ATAC , printed on 04/02/2025

SC_ATAC_COUNTER_CSSC_ATAC_COUNTERATAC_CLOUPE_PREPROCESSATAC_COUNTER_PREFLIGHTATAC_COUNTER_PREFLIGHT_LOCAL_BASIC_SC_ATAC_COUNTERATAC_SETUP_CHUNKSFILTER_PEAK_MATRIX_ATAC_MATRIX_COMPUTERALIGN_ATAC_READSGENERATE_PEAK_MATRIXMAKE_ATAC_SHARDSMARK_ATAC_DUPLICATESWRITE_ATAC_BAM_PEAK_CALLERCONVERT_SIGNAL_TRACKCOUNT_CUT_SITESDETECT_PEAKS_PRODUCE_CELL_BARCODESDETECT_CELL_BARCODESMERGE_CELL_METRICSMERGE_EXCLUDED_BARCODESREMOVE_BARCODE_MULTIPLETSREMOVE_GEL_BEAD_DOUBLET_BARCODESREMOVE_LOW_TARGETING_BARCODES_SC_ATAC_ANALYZERATAC_ANALYZER_PREFLIGHTATAC_COMBINE_CLUSTERINGATAC_RUN_GRAPH_CLUSTERINGATAC_SUMMARIZE_ANALYSISCLUSTER_CELLSPERFORM_DIFFERENTIAL_ANALYSISREDUCE_DIMENSIONSRUN_MANIFOLD_PROJECTION_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_COUNTER_CS

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