Maintenance
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add_att_b_sites Add attB Sites |
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add_fold_changes_to_variant |
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add_info_overlapping_genes Add Information from Overlapping Genes |
Add Fold Changes |
alignment |
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amino_acid_changes Amino Acid Changes |
Create Alignment |
annotate_conservation_score |
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annotate_exon_numbers Annotate with Exon Numbers |
Annotate with Conservation Scores |
annotate_from_known_variants |
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annotate_nearby_gene Annotate with Nearby Gene Information |
Annotate from Known Variants |
annotate_overlapping |
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annotate_variant_flank Annotate with Flanking Sequences |
Annotate with Overlap Information |
assemble_sanger_sequences |
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associate_metadata Associate Data with Metadata |
Assemble Sequences |
basic_variant_detection |
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bisulfite_call_methylation_levels Call Methylation Levels |
Basic Variant Detection |
bisulfite_create_rrbs_track |
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bisulfite_read_mapping Map Bisulfite Reads to Reference |
Create RRBS-fragment Track |
blast |
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blast_make_db Create BLAST Database |
BLAST |
blast_ncbi |
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boxplot Create Boxplot |
BLAST at NCBI |
bp_reaction |
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clustering_of_samples Hierarchical Clustering of Samples |
Create Entry Clone (BP) |
cnv_detection |
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compare_sample_variant_tracks Compare Sample Variant Tracks |
CNV Detection |
compare_variants_within_group |
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consensus_sequence_extraction Extract Consensus Sequence |
Identify Shared Variants |
contig_read_mapping |
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convert_from_tracks Convert from Tracks |
Map Reads to Contigs |
convert_to_dna |
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convert_to_rna Convert DNA To RNA |
Convert RNA to DNA |
convert_to_tracks |
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coverage_analysis Whole Genome Coverage Analysis |
Convert to Tracks |
create_combined_rnaseq_report |
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create_expression_browser Create Expression Browser |
Create Combined RNA-Seq Report |
create_fc_from_expr_tracks_algo |
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create_heatmap_for_rnaseq Create Heat Map for RNA-Seq |
Create fold change track from expressions |
create_histogram |
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create_sequence_statistics Sequence statistics |
Create Histogram |
create_track_list |
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create_venn_diagram_for_rnaseq Create Venn Diagram for RNA-Seq |
Create Track List |
denovo_assembly |
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detailed_mapping_report QC for Read Mapping |
De Novo Assembly |
differential_expression_rna_seq |
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differential_expression_two_groups Differential Expression in Two Groups |
Differential Expression for RNA-seq |
download_genome |
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download_pfam_database Download Pfam Database |
Download Genome |
download_sequence_to_structure_db |
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download_sra SRA Download |
Download 3D Protein Structure Database |
duplicate_mapped_reads_removal |
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empirical_analysis_dge Empirical Analysis of DGE |
Duplicate Mapped Reads Removal |
experiment_to_track |
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extract_annotations Extract Annotations |
Create Track from Experiment |
extract_overlapping_reads |
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extract_sequences Extract Sequences |
Extract Reads |
filter_against_control_reads |
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filter_against_known_variants Filter against Known Variants |
Remove Variants Present in Control Reads |
filter_annotation_names |
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filter_marginal_variants Remove Marginal Variants |
Filter Annotations on Name |
filter_overlapping |
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filter_reference_variants Remove Reference Variants |
Filter Based on Overlap |
find_open_reading_frames |
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find_primer_binding_sites Find Binding Sites and Create Fragments |
Find Open Reading Frames |
fisher_exact_test |
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fixed_ploidy_variant_detection Fixed Ploidy Variant Detection |
Identify enriched variants in case vs control samples |
gaussian_statistical_analysis |
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gc_contents_graph_track Create GC Content Graph Track |
Gaussian Statistical Analysis |
gene_set_test |
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go_analysis_expression_change Identify Differentially Expressed Gene Groups and Pathways |
Gene Set Test |
go_enrichment_variants |
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graph_threshold Identify Graph Threshold Areas |
GO Enrichment Analysis |
identify_candidate_variants_new |
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import_metadata_rows Import Metadata rows into Metadata Table |
Filter Variants on Custom Criteria |
import_tracks |
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kmer_tree_construction K-mer Based Tree Construction |
Import Tracks from File |
link_to_structure |
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local_realignment Local Realignment |
Link Variants to 3D Protein Structure |
low_frequency_variant_detection |
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lr_reaction Create Expression Clone (LR) |
Low Frequency Variant Detection |
ma_plot |
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mapping_graph_tracks Create Mapping Graph Tracks |
Create MA Plot |
merge_annotation_tracks |
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merge_mappings Merge Read Mappings |
Merge Annotation Tracks |
merge_overlapping_pairs |
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ml_phylogeny Maximum Likelihood Phylogeny |
Merge Overlapping Pairs |
model_testing |
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motif_search Motif Search |
Model Testing |
mutation_tester_tool |
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new_sequence_list Sequence List |
Identify Known Mutations from Mappings |
ngs_connector_import |
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ngs_import_fasta Fasta High-Throughput Sequencing Import |
Import NGS sample reads |
ngs_import_genereader |
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ngs_import_illumina Illumina High-Throughput Sequencing Import |
QIAGEN GeneReader Sequencing Import |
ngs_import_iontorrent |
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ngs_import_pacbio PacBio High-Throughput Sequencing Import |
Ion Torrent High-Throughput Sequencing Import |
ngs_import_roche454 |
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ngs_import_sam Import SAM/BAM Mapping Files |
Roche 454 High-Throughput Sequencing Import (legacy) |
ngs_import_sanger |
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peak_shape_chip_seq_analysis Transcription Factor ChIP-Seq |
Sanger High-Throughput Sequencing Import |
pfam_domain_search |
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predict_splice_site Predict Splice Site Effect |
Pfam domain search |
primer_pair_import |
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principal_component_for_rna_seq PCA for RNA-Seq |
Primer Pair Import |
principal_components |
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process_tagged_sequences Demultiplex Reads |
Principal Component Analysis |
proportion_statistical_analysis |
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read_mapping Map Reads to Reference |
Proportion-based Statistical Analysis |
reference_assemble_sanger_sequences |
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remove_information_from_variants Remove Information from Variants |
Assemble Sequences to Reference |
remove_orphan_reference_variants |
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reverse_complement_sequence Reverse Complement Sequence |
Remove Orphan Reference Variants |
reverse_sequence |
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rna_seq RNA-Seq Analysis |
Reverse Sequence |
sample_reads |
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secondary_peak_calling Secondary Peak Calling |
Sample Reads |
sequencing_qc_report |
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small_rna_annotate Annotate and Merge Counts |
QC for Sequencing Reads |
small_rna_sampling |
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spikein_control_import RNA Spike-ins |
Extract and Count |
statistics_target_regions |
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structural_variant_detection InDels and Structural Variants |
QC for Targeted Sequencing |
translate_to_protein |
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tree_construction Create Tree |
Translate to Protein |
trim |
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trio_analysis TRIO analysis |
Trim Reads |
xy_scatter_plot |
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Core tasks |
Create Scatter Plot |
export |
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import Import files on server (excluding NGS import) |
Export files from server |
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chmod Change permissions on folders |
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cp |
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empty_recycle_bin Empty recycle bin on data location |
Copy source files and/or directories to destination directory |
history |
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list_data_locations List all data locations on server |
Show history of selected files |
list_import_locations |
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ls List files in directories |
List all High-throughput sequencing data import locations |
mkdir |
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move Move source files and/or directories to destination directory |
Make directories |
mv |
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rename Rename files and directories |
Move source files and/or directories to destination directory |
rm |
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search Search for files on server |
Remove files and/or directories |
Direct |
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blast_delete_index Delete blast index |
Commands |
blast_get_db_locations |
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blast_get_indexes Get blast indexes |
Get Blast DB Locations |
blast_list_index_files |
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blast_set_db_locations Set blast database locations |
List index files in the given database |
Maintenance |
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disable_maintenance_mode Disable server maintenance mode |
(only for admin users) |
enable_maintenance_mode |
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install_plugin_and_restart Install plugin(s) and restart the server and any attached job nodes |
Enable server maintenance mode |
install_workflow |
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list_plugins Lists installed plugins |
Install workflow(s) |
list_workflows |
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restart_server Restart server and any attached job nodes |
Lists installed workflows |
shutdown_server |
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uninstall_plugin_and_restart Uninstall plugin(s) and restart the server and any attached job nodes |
Shut down the server and any attached job nodes |
uninstall_workflow |
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> |
Uninstall workflow(s) |