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10x Genomics
Single Cell ATAC

Cell Ranger ATAC , printed on 04/02/2025

SC_ATAC_COUNTER_CSSC_ATAC_COUNTERATAC_COUNTER_PREFLIGHTATAC_COUNTER_PREFLIGHT_LOCALCLOUPE_PREPROCESS_BASIC_SC_ATAC_COUNTERFILTER_PEAK_MATRIXGENERATE_PEAK_MATRIX_ALIGNERALIGN_READSSETUP_CHUNKSTRIM_READS_PEAK_CALLERCOUNT_CUT_SITESDETECT_PEAKS_PRODUCE_CELL_BARCODESDETECT_CELL_BARCODESMERGE_CELL_METRICSMERGE_EXCLUDED_BARCODESREMOVE_BARCODE_MULTIPLETSREMOVE_GEL_BEAD_DOUBLET_BARCODESREMOVE_LOW_TARGETING_BARCODES_SORT_AND_MARK_DUPSATTACH_BCSMARK_DUPLICATESSORT_READS_BY_POS_SC_ATAC_ANALYZERANALYZER_PREFLIGHTCLUSTER_CELLSCOMBINE_CLUSTERINGPERFORM_DIFFERENTIAL_ANALYSISPROJECT_TSNEREDUCE_DIMENSIONSRUN_GRAPH_CLUSTERINGSUMMARIZE_ANALYSIS_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_COUNTER_CS

Wraps the main pipeline to produce the final output files