• Manuals

Browse the manual

• Introduction
  • Installation
• Basic usage
  • Handling passwords
  • Managing SSL certificates
  • Data objects, data files and the CLC URL
    • The CLC URL - the ID form
    • The CLC URL - name form
    • Indicating local system files or folders
  • Result files and connecting analyses in pipelines
  • Executing workflows
  • Emptying the recycling bin for a CLC Server File Location
• Usage for CLC Genomics Server
  • Algorithms
    • add_att_b_sites
    • add_fold_changes_to_variant
    • add_info_overlapping_genes
    • alignment
    • amino_acid_changes
    • annotate_conservation_score
    • annotate_exon_numbers
    • annotate_from_known_variants
    • annotate_nearby_gene
    • annotate_overlapping
    • annotate_variant_flank
    • assemble_sanger_sequences
    • associate_metadata
    • basic_variant_detection
    • bisulfite_call_methylation_levels
    • bisulfite_create_rrbs_track
    • bisulfite_read_mapping
    • blast
    • blast_make_db
    • blast_ncbi
    • boxplot
    • bp_reaction
    • clustering_of_samples
    • cnv_detection
    • compare_sample_variant_tracks
    • compare_variants_within_group
    • consensus_sequence_extraction
    • contig_read_mapping
    • convert_from_tracks
    • convert_to_dna
    • convert_to_rna
    • convert_to_tracks
    • coverage_analysis
    • create_combined_rnaseq_report
    • create_expression_browser
    • create_fc_from_expr_tracks_algo
    • create_heatmap_for_rnaseq
    • create_histogram
    • create_sequence_statistics
    • create_track_list
    • create_venn_diagram_for_rnaseq
    • denovo_assembly
    • detailed_mapping_report
    • differential_expression_rna_seq
    • differential_expression_two_groups
    • download_genome
    • download_pfam_database
    • download_sequence_to_structure_db
    • download_sra
    • duplicate_mapped_reads_removal
    • empirical_analysis_dge
    • experiment_to_track
    • extract_annotations
    • extract_overlapping_reads
    • extract_sequences
    • filter_against_control_reads
    • filter_against_known_variants
    • filter_annotation_names
    • filter_marginal_variants
    • filter_overlapping
    • filter_reference_variants
    • find_open_reading_frames
    • find_primer_binding_sites
    • fisher_exact_test
    • fixed_ploidy_variant_detection
    • gaussian_statistical_analysis
    • gc_contents_graph_track
    • gene_set_test
    • go_analysis_expression_change
    • go_enrichment_variants
    • graph_threshold
    • identify_candidate_variants_new
    • import_metadata_rows
    • import_tracks
    • kmer_tree_construction
    • link_to_structure
    • local_realignment
    • low_frequency_variant_detection
    • lr_reaction
    • ma_plot
    • mapping_graph_tracks
    • merge_annotation_tracks
    • merge_mappings
    • merge_overlapping_pairs
    • ml_phylogeny
    • model_testing
    • motif_search
    • mutation_tester_tool
    • new_sequence_list
    • ngs_connector_import
    • ngs_import_fasta
    • ngs_import_genereader
    • ngs_import_illumina
    • ngs_import_iontorrent
    • ngs_import_pacbio
    • ngs_import_roche454
    • ngs_import_sam
    • ngs_import_sanger
    • peak_shape_chip_seq_analysis
    • pfam_domain_search
    • predict_splice_site
    • primer_pair_import
    • principal_component_for_rna_seq
    • principal_components
    • process_tagged_sequences
    • proportion_statistical_analysis
    • read_mapping
    • reference_assemble_sanger_sequences
    • remove_information_from_variants
    • remove_orphan_reference_variants
    • reverse_complement_sequence
    • reverse_sequence
    • rna_seq
    • sample_reads
    • secondary_peak_calling
    • sequencing_qc_report
    • small_rna_annotate
    • small_rna_sampling
    • spikein_control_import
    • statistics_target_regions
    • structural_variant_detection
    • translate_to_protein
    • tree_construction
    • trim
    • trio_analysis
    • xy_scatter_plot
  • Core tasks
  • Dataoperations
    • chmod
    • cp
    • empty_recycle_bin
    • history
    • list_data_locations
    • list_import_locations
    • ls
    • mkdir
    • move
    • mv
    • rename
    • rm
    • search
  • Direct Commands
    • blast_delete_index
    • blast_get_db_locations
    • blast_get_indexes
    • blast_list_index_files
    • blast_set_db_locations
    • Maintenance
    • disable_maintenance_mode
    • enable_maintenance_mode
    • install_plugin_and_restart
    • install_workflow
    • list_plugins
    • list_workflows
    • restart_server
    • shutdown_server
    • uninstall_plugin_and_restart
    • uninstall_workflow
  • Importers
    • ace
    • automaticimport
    • blast_db
    • bsml
    • cas
    • chp
    • clc
    • clustalw
    • cm5
    • embl
    • excel
    • expression_annotation
    • expression_data_table
    • expressionarray
    • externalfile
    • fasta
    • fasta_alignment
    • gcg
    • gck
    • genbank
    • gene_ontology
    • illumina_annotation
    • illumina_expression
    • lasergene
    • mir_base
    • msf
    • netaffx
    • newick
    • nexus
    • pdb_import
    • phylib
    • pir
    • raw_sequence
    • rna_structure
    • sam_bam
    • sequence_csv
    • soft_geo_sample
    • soft_geo_series
    • staden
    • strider
    • swissprot
    • table_csv
    • text
    • trace
    • trim_adapter_list
    • zip
  • Exporters
    • ace
    • annotation_csv
    • annotation_excel_1997_2007
    • annotation_excel_exporter_2010
    • annotation_tsv
    • bam
    • bed
    • clc
    • clustalw
    • col
    • contig_agp
    • ct
    • embl
    • excel_1997_2007
    • excel_2010
    • fasta
    • fasta_alignment
    • fastq
    • genbank
    • gff3
    • gtf
    • gvf
    • history_csv
    • history_pdf
    • html_export
    • mapping_tsv
    • msf
    • newick
    • nexus
    • phylip
    • pir
    • rnaml
    • sam
    • scf
    • sequence_csv
    • strider
    • swissprot
    • table_csv
    • text
    • tsv
    • vcf
    • wiggle
    • zip

Core tasks

export	Export files from server
import	Import files on server (excluding NGS import)

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