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Data Upload definitions


Ingenuity Pathway Analysis (IPA) | Definitions for the Data Upload workflow

Version number or Date of Third Party Databases


Ingenuity Pathway Analysis (IPA)

MAP-Molecule Activity Predictor


Ingenuity Pathway Analysis (IPA)

Molecule View


Ingenuity Pathway Analysis (IPA) | Description of the molecule tab in Core Analysis

Listing of Networks


Ingenuity Pathway Analysis (IPA) | Listing of Networks

Core, Tox and Metabolomic Comparison Analysis


Ingenuity Pathway Analysis (IPA)

FAQ - Analysis Match


Ingenuity Pathway Analysis (IPA)

Accessing and Using Downstream Effects Analysis


Ingenuity Pathway Analysis (IPA)

microRNA Target Filter FAQ


Ingenuity Pathway Analysis (IPA) | FAQs about the microRNA Target Filter

Formatting Your Dataset


Ingenuity Pathway Analysis (IPA)

Identifier and Gene Model Source Versions


Ingenuity Pathway Analysis (IPA) | The versions of the identifier and gene model databases used in IPA currently

My Libraries


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Variants Table Columns and Annotations


Ingenuity Variant Analysis | Variants, Annotation, Allele Fraction, SIFT, Genotype (IVA)

IPA Video Tutorials


Ingenuity Pathway Analysis (IPA) | Summary of available video tutorials for IPA

Pathway Activity Overlay


Ingenuity Pathway Analysis (IPA) | Pathway Activity Overlay (part of Pathway Activity Analysis performed within a core analysis)

Upstream Regulator Analysis


Ingenuity Pathway Analysis (IPA) | More info link for URA master table

Canonical Pathways for a Dataset


Ingenuity Pathway Analysis (IPA) | Canonical Pathways for a Dataset

Isoforms View


Ingenuity Pathway Analysis (IPA) | Isoform view on Gene Views

Can I use more than one identifier type?


Ingenuity Pathway Analysis (IPA) | A dataset file may contain more than one of the identifier type. If your dataset file has more than one identifier type, select all appropriate identifier types found in the dataset file from the dropdown menu.

Copy Number Analysis


Key words: copy number variant, copy number variants, CNV (IVA)

Comparison analysis heat map for Diseases and Functions


Ingenuity Pathway Analysis (IPA) | Comparison Analysis heat map for Disease and Functions

Variant Analysis Supported file formats


File formats supported in Ingenuity Variant Analysis (IVA)

Eligible Pathways List


Canonical Pathways (signaling) that are currently eligible for Pathway Activity Analysis

Available Canonical Pathways


Ingenuity Pathway Analysis (IPA) | Currently Available Canonical Pathways

How to Chart Diseases and Functions Comparison Data in Excel


Ingenuity Pathway Analysis (IPA)

FAQ - Statistical Calculation


Ingenuity Pathway Analysis (IPA)

Spring IPA Release notes, March 2019


Summary of Release Notes

Spotfire Integration with IPA


Ingenuity Pathway Analysis (IPA)

How to Chart Comparison Analysis Using Excel


Ingenuity Pathway Analysis (IPA)

Comparison analysis heat map for canonical pathways


Comparison analysis heat map for canonical pathways

IPA-Tox Analysis Workflow


Ingenuity Pathway Analysis (IPA)

Running-IPA-on-Mac


Ingenuity Pathway Analysis (IPA) | This article is about running IPA on a Mac. FAQ, Caches and Version of Mac OS and Java

FAQs on Analytics


Ingenuity Variant Analysis | Sex Assignment, Inferred Activity (IVA)

Ratio Calculations for Pathways


Ingenuity Pathway Analysis (IPA)

IPA Network Generation Algorithm


Ingenuity Pathway Analysis (IPA)

Right Click Menu


Ingenuity Pathway Analysis (IPA)

Graph Preferences


Ingenuity Pathway Analysis (IPA)

Cache


Ingenuity Pathway Analysis (IPA)

BioProfiler


Ingenuity Pathway Analysis (IPA) | Advanced Analytics BioProfiler

Relationship Export


Ingenuity Pathway Analysis (IPA) | Relationship Export

Add My Findings


Ingenuity Pathway Analysis (IPA) | Add My Findings from the Build Tool

Comparison analysis heat map for causal networks


Ingenuity Pathway Analysis (IPA)

Causal Networks


Ingenuity Pathway Analysis (IPA) | Advanced Analytics - Generate virtual upstream regulators which are networks of regulators

My Findings


Ingenuity Pathway Analysis (IPA) | My Findings

Application Preferences


Ingenuity Pathway Analysis (IPA)

IsoProfiler Findings


Ingenuity Pathway Analysis (IPA) | Examine the detailed relationships between isoforms (splice variants) and known diseases and functions.

IPA Network Generation Algorithm Whitepaper


Ingenuity Pathway Analysis (IPA) | Whitepaper Link

Running-IPA-on-Windows


Ingenuity Pathway Analysis (IPA) | Running IPA on Windows

IsoProfiler


Ingenuity Pathway Analysis (IPA) | IsoProfiler displays and enables filtering on transcripts & isoforms in your RNA-seq dataset(s)

IPA installer


Ingenuity Pathway Analysis (IPA) | How to use the IPA client installer

FAQ - Causal Network Analysis


Ingenuity Pathway Analysis (IPA)

My Findings Overview


Ingenuity Pathway Analysis (IPA) | How to Format and Upload custom findings data file in IPA

IPA Technical Requirements


Ingenuity Pathway Analysis (IPA) | IPA Technical Requirements

Project Manager


Ingenuity Pathway Analysis (IPA)

IPA Glossary


Ingenuity Pathway Analysis (IPA)

IPA Toolbar Menus


Ingenuity Pathway Analysis (IPA)

Dataset and Analysis Search


Ingenuity Pathway Analysis (IPA) | Search Project Manager for Analysis and Dataset

IPA Legend


Ingenuity Pathway Analysis (IPA) | Describes the tool bar icons, colors, and more in IPA

How can I evaluate the software and how long is the evaluation period?


Information about free evaluation licenses for the CLC Workbenches

How can I cite CLC bio Workbenches and Servers in my paper?


Citation guidelines for the CLC Workbenches

How can I submit a feature request?


Describes how to find out if a particular feature is already available in the Workbench and how to submit a feature request

What happens to my data after the evaluation period if I don't purchase the software?


How to work with data that was generated in a Workbench after the evaluation period

Are all features of the software available during an evaluation?


Describes which functionality is available for trial users of a Workbench

How can a reviewer or colleague view my results if they don't have a license for the software?


Description of the "Viewing Mode" of the CLC Workbenches

How do I submit an error report for a CLC License Server to the CLC Support team?


How do I submit an error report for a CLC License Server to the CLC Support team?

How do I submit an error report for a CLC Genomics Server to the CLC Support team?


CLC Genomics Server | How do I submit an error report for a CLC Genomics Server to the CLC Support team?

CLC Workbench error report submission to the Support team


How do I submit an error report for a CLC Workbench to the Support team?

Accessing and Using Upstream Regulators


What is the host ID for a machine running the CLC Genomics Server software?


CLC Genomics Server | How to find the host ID for a computer running CLC Genomics Server

How do I get a new static license when upgrading between major software versions?


CLC Genomics Workbench | Upgrading static licenses between major software versions

Where is my license file?


CLC Genomics Workbench | Where is the location of a license file for CLC software

Can I move my CLC software license to a different machine?


CLC Genomics Workbench | Background information and instructions for moving a CLC software license to a different computer.

Data Source Filter


Upstream Regulators Analysis Tutorial


Ingenuity Pathway Analysis (IPA)

Search for Genes Tutorial


Ingenuity Pathway Analysis (IPA)

Upload and Analyze Example Data Tutorial


Ingenuity Pathway Analysis (IPA)

Human Isoforms View Tutorial


Ingenuity Pathway Analysis (IPA)

Visualize Pathways Tutorial


Ingenuity Pathway Analysis (IPA)

Data Upload workflow


Ingenuity Pathway Analysis (IPA) | Data Upload workflow

Which internet addresses does CLC software need access to?


CLC Genomics Workbench

upload-analyze-your-data-tutorial


Ingenuity Pathway Analysis (IPA)

Filtered and Annotated Datasets


Ingenuity Pathway Analysis (IPA)

FAQs on HumanCyc Database


FAQs on HumanCyc Database

Link for CLC Product FAQs


CLC Genomics Workbench | Please find the link to the CLC product FAQs in this article.

Downstream Effects Analysis Tutorial


Ingenuity Pathway Analysis (IPA)

Biomarker Analysis


File Format Specification for Uploading Data with Experimental Metadata into IPA


Ingenuity Pathway Analysis (IPA) | Experimental Metadata Specifications

FAQ - Ingenuity Knowledge Base


Batch Upload


Ingenuity Pathway Analysis (IPA) | How to upload multiple datasets as a batch

Publish using Ingenuity Variant Analysis


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Usual Suspects Option in the Confidence Filter


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Counteract variants effect on known signaling pathways


Ingenuity Variant Analysis | drugs, signaling pathway, druggable, counteract (IVA)

Pathways Interpretation


Ingenuity Variant Analysis | pathways interpretation, significant pathways, pathways association, signaling pathways, druggable pathways (IVA)

Export in Variant Analysis


Ingenuity Variant Analysis | Exporting, VCF export, Tab-delimited file, PNG, Pathway Export (IVA)

The Ingenuity Knowledge Base for Variant Analysis


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Cancer Driver Variants Filter


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Variant Analysis Technical Requirements


Ingenuity Variant Analysis | Technical Requirements for Variant Analysis (IVA)

Creating an Analysis in Variant Analysis


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Glossary for Variant Analysis


Ingenuity Variant Analysis | Gene model, mitochondrial genes, mitochondria, promoter (IVA)

User Defined Variants in Variant Analysis


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Physical Location Filter


Ingenuity Variant Analysis | Ingenuity variant Analysis (IVA)

Pathway Legend


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Sharing in Variant Analysis


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Pharmacogenetics Filter


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Custom Annotation


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Quantitative Trait Tutorial


Ingenuity Variant Analysis | Quantitative Trait, Clinical Features, Clinical Trait, Trait, QT (IVA)

Ingenuity Variant Analysis and Biobase HGMD integration


Ingenuity Variant Analysis | Biobase, HGMD, Integration (IVA)

Variant Analysis License Agreement and Privacy Policy


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Training and Scientific Seminars


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Citing Ingenuity Variant Analysis


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Upload your Sample


Ingenuity Variant Analysis | How to upload, metadata, datastream uploader (IVA)

Ingenuity Inferred Activating Mutations Algorithm


Ingenuity Variant Analysis | inferred, mutation, gain of function (IVA)

Causal Network Analysis in the Biological Context Filter


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Statistical Association


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Pre-Filtering of samples


Ingenuity Variant Analysis | WGS, pre-filter, whole genome sequencing (IVA)

Common Variants Filter


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Biological Context


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Genetic Analysis Filter


Ingenuity Variant Analysis | mendelian, inheritance, transmitted, co-segregation, genotype (IVA)

Filtering for X-linked recessive diseases in a trio


Ingenuity Variant Analysis | X-linked, trio (IVA)

Confidence Filter


Ingenuity Variant Analysis | Call Quality, Upstream Pipeline, Read Depth, Allele Fraction, Genotype Quality, and Usual Suspects (IVA)

Exploring Your Results in Variant Analysis


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Phenotype-Driven Ranking Filter


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

How To Add and Use Sample Metadata


Ingenuity Variant Analysis | Sample MetaData, Pedigrees, Clinical Annotation, Subject Identifiers (IVA)

FAQs about Statistical Calculation


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Predicted Deleterious Filter


Ingenuity Variant Analysis | Ingenuity Variant Analysis (IVA)

Analysis Results Tutorial


Ingenuity Pathway Analysis (IPA)

Analysis Match


Core Analysis tab that displays related analyses (among thousands of curated analyses) based on shared pattern of predicted "entities" like Upstream Regulators, Canonical Pathways, etc.

Contact CLC specialists on the QIAGEN support team.


CLC Genomics Workbench | How do I contact the CLC specialist on the QIAGEN Advanced Genomics Support team?

How can I see the pathways related to this analysis


How can I see the pathways related to this analysis?

Terminological difference between GeneGlobe Data Analysis Center and Biomedical Genomics Workbench


Biomedical Genomics Workbench | Where are "read fragments per MT mean" and "mean MT" in the results of QIAseq Targeted Panel Analysis Plugin of Biomedical Genomics Workbench (BxWB)?

Defining the Reference Set


Ingenuity Pathway Analysis (IPA)

Reference set array platforms


Reference Set Array platforms in IPA

Pathway and Network Explorer Toolbar


List Analysis


Regulator Effects


Regulator Effects

Advanced Settings


Describes the Advanced Settings available to customize a Core Analysis

Legend Tool


Describes how to add a legend to a Path Designer pathway

Interpreting the Upstream Regulator Results


Where can I find the manual?


CLC Genomics Workbench

Why can't I see the Workbench even though it is running on my Windows system?


CLC Genomics Workbench

Why is my Workbench taking so long to start up?


CLC Genomics Workbench

Which tasks require me to run the Workbench as an administrative user and how?


CLC Genomics Workbench

Will a high spec graphics card improve CLC Workbench performance?


CLC Genomics Workbench

Why does the Workbench 3D Viewer throw a OpenGL error suggeting that my graphics card needs updating?


CLC Genomics Workbench

Why do I see a JVM error when I start up the Workbench?


CLC Genomics Workbench

Why is the Workbench sometimes slow on OS X Mavericks and later versions?


CLC Genomics Workbench

How can I install plugins in a CLC Workbench?


CLC Genomics Workbench

How can I install plugins in a CLC Server?


CLC Genomics Server

Why are no plugins listed in Download Plugins tab of the Plugins Manager?


CLC Genomics Workbench

Ingenuity Knowledge Base


How are networks calculated?


How are networks calculated?

Why is the Workbench/Server holding onto memory between jobs?


CLC Genomics Workbench

Where can I get installer files for the software?


CLC Genomics Workbench

How do I change the memory limit for the CLC Workbench or Server java process?


CLC Genomics Workbench

Where should I install an upgrade to my CLC Genomics Server software?


CLC Genomics Server

How do I install or upgrade my Workbench on a non-networked machine?


CLC Genomics Workbench

How can I uninstall a CLC Workbench?


CLC Genomics Workbench

How do I download the software if I get a message about the signature being corrupt or invalid?


CLC Genomics Workbench

How can I get a copy of the Software Developer Kit?


CLC Genomics Workbench

Where is my CLC Workbench data?


CLC Genomics Workbench

How can I move my CLC data?


CLC Genomics Workbench

How can I set a different default location for data to be saved into?


CLC Genomics Workbench

Why is my data location greyed out in the Workbench navigation area?


CLC Genomics Workbench

What Linux distributions do you support?


CLC Genomics Workbench

Where should I install an upgrade to my CLC Workbench software?


CLC Genomics Workbench

Where are my temporary files to be written to and how can I change this?


CLC Genomics Workbench

Why are temporary files still written to the old default location after I redirect them?


CLC Genomics Workbench

What does an error about problems writing to temp mean?


CLC Genomics Workbench

How can I delete a whole data location and all its contents?


CLC Genomics Workbench

What is the difference between running a Genomics Server and running a Genomics Workbench on a large central machine that multiple users can access?


CLC Genomics Workbench

Are the tools of the CLC Workbenches or Servers multi-threaded?


CLC Genomics Workbench

Where is my user settings file?


CLC Genomics Workbench

Where are the Workbench logfiles?


CLC Genomics Workbench

What does it mean if a Mac installer says it "is damaged and can't be opened"?


CLC Genomics Workbench

How can I find research papers on a given topic?


How can I find research papers on a given topic?

Why has Download Genome failed in the CLC Genomics Workbench?


CLC Genomics Workbench | This FAQ includes different reasons why the Download Genome tool may fail in the Genomics Workbench and guidelines on how to resolve the issue

Why is my data import failing?


CLC Genomics Workbench | This FAQ describes different reasons why import of your data into the Workbench(es) are failing.

How can I install the CLC Workbench on a Linux system using the installer script?


CLC Genomics Workbench

How can I upgrade my CLC Workbench?


CLC Genomics Workbench

Why isn't my Genbank file accepted for import?


CLC Genomics Workbench | This article lists possible reasons why a Genbank import into the Workbench might fail.

How can I import files containing interleaved paired data?


CLC Genomics Workbench | This FAQ includes instructions about how to import a single interleaved paired-end sequencing data

How can I check if my data file is corrupt?


CLC Genomics Workbench | This FAQ includes information about checking integrity of a file before

Overlapping Canonical Pathways


Canonical Pathways Overview


An Overview of the Canonical Pathways in IPA

Interpreting Functional Analysis Results


Shared With Others


Can I run a local BLAST search against multiple blast databases simultaneously?


CLC Genomics Workbench

Can I find mutations associated with two (or more) phenotypes in HGMD®?


HGMD Online

In the quick search part of the HGMD® Advanced search, what does the ranking score relate to?


HGMD Online | Description of the Ranking Score used in the Quick Search of HGMD® Advanced

Which genome build are you currently using for mapping HGMD® mutations?


HGMD Online | Information about the genome build used in HGMD®

The HGMD® application lists multiple articles per ALLMUT record. Where are these stored and will all papers specified for an ALLMUT record be in agreement about the risk allele?


HGMD Download | Describes how to find additional references in the HGMD® download version

How to perform a batch search in HGMD®?


HGMD Online

Is the article/paper identified by the PMID in an ALLMUT record one of the studies that established the genetic association with the disease/phenotype?


HGMD Download | Description of the PMID column of the ALLMUT table (HGMD® download version)

Two new germinal mutations recently identified in our lab, are not reported in the HGMD® database. How can they be added?


HGMD Online

Why do numbers for sequences in HGMD® differ from numbering in (primary) references?


HGMD Online

How does the HGMD® define a genomic alteration as a mutation or a polymorphism?


HGMD Online

Do you include variants from genome-wide association studies (GWAS) papers in HGMD®?


HGMD Online

Which strand are the sequences in the HGMD® database taken from?


HGMD Online

Is the risk allele for a given site-disease association available (or derivable from data) in the HGMD database?


HGMD Online

Is the first position in a chromosome counted as "0" or "1" for the purpose of determining genomic coordinates?


HGMD Online | Chromosome coordinate system used in HGMD®

How do I interpret the MutPred score and the MutPred hypothesis?


HGMD Online

What is MutPred?


HGMD Online

What is SIFT?


HGMD Online | Description of the SIFT algorithm

How do I interpret the SIFT score?


HGMD Online

Is there a way to get a complete SNP list for a gene, including mutations which are not disease-causing?


HGMD Online

How does the HGMD® database represent a simple, single-base insertion?


HGMD Online

How do I obtain the MutPred scores from the HGMD® download version?


HGMD Online

Why does the description of a deletion not always match between the mutation description, the HGVS nomenclature, and the VCF format?


HGMD Online | Why does the lower case "acag" representation in TACTAC^414TTAGacagAGAAGCTGGG not match the c.1245_1248delCAGA position for the deletion CD982750 in SMAD4?

How may I find the location of mutations in a specific splice variant for genes with multiple splicing variants?


HGMD Online | Is the codon numbering system for different mutations in a gene consistent, i.e. is the numbering for different mutations all based on one splicing variant? If yes, where could I find the accession number of this mRNA splicing variant?

Does the HGMD® provide any information regarding polymorphisms found in human genes?


HGMD Online

How frequently is the HGMD® database updated?


HGMD Online

How should I reference HGMD® Professional in a scientific article?


HGMD Online | Citation guidelines for HGMD® Professional

How do you decide which reference cDNA to link to a gene entry in HGMD®?


HGMD Online

In HGMD®, there are some common SNPs listed as mutations. Are you going to correct these?


HGMD Online

What do I do if I end up with .zip files instead of .cpa files when I download plugins from the website?


CLC Genomics Workbench

Can I run CLC Workbench software on a machine that is not network connected?


CLC Genomics Workbench

Can I limit the number of CPUs used by a CLC Workbench?


CLC Genomics Workbench

Where is my Workbench installation directory?


CLC Genomics Workbench

Why are annotations black when I export to eps format?


CLC Genomics Workbench | This FAQ covers why annotations appear black when exported in eps and what you can do to correct this.

Can I rearrange the layout of a sequence or alignment for publishing?


CLC Genomics Workbench | The FAQ covers how you can rearrange a sequence or alignment or other elements in exported image for publishing purposes

How can I import mappings from a SAM/BAM file where the reference names are different to those in the Workbench?


CLC Genomics Workbench | This FAQ covers guidelines on how to import SAM/BAM file whose reference names are different than those present in the Workbench

Can I install a CLC Genomics Workbench on a compute cluster?


CLC Genomics Workbench

What does "error code 34" mean when I run the installer?


CLC Genomics Workbench

How can I add a new data location to the Navigation Area?


CLC Genomics Workbench

Why is the output either too big or too small when I print, compared to what I see on screen?


CLC Genomics Workbench | This FAQ covers how you can print your image in the correct size

How do I import a cas format file from the Assembly Cell into a workbench?


CLC Genomics Workbench | This FAQ explains how you can import .cas format file obtained from Assembly Cell into the Genomics and Biomedical Genomics Workbench

How can I import sequence reads in a SAM or BAM file?


CLC Genomics Workbench | This FAQ covers information regarding import of sequencing reads in a SAM or BAM file

Why do I run out of memory when importing a BAM file containing paired data?


CLC Genomics Workbench | This FAQ provides an explanation about why you may run of memory while trying to import a BAM or SAM file

How can I import a BAM file containing data mapped to the hg19 UCSC genome?


CLC Genomics Workbench | This FAQ covers how you can import a BAM file mapped to hg19 UCSC genome and the differences between hg19 genome obtained from UCSC vs. Ensembl or Genbank

Why are no BLAST databases listed in the Download BLAST Databases window?


CLC Genomics Workbench | This FAQ describes the reason why you may not see any BLAST databases in the Download BLAST Databases window and workarounds to obtain the databases

Cell Art


Description of the Cell Art tool of Path Designer

How can I evaluate the software on a non-networked machine?


CLC Genomics Workbench | Describes how to obtain an evaluation license for a machine that does not have a network connection

How do I transfer data using ftp details you've sent?


CLC Genomics Workbench | Transfer data for troubleshooting to an ftp area that was set up by the support team

Am I eligible for support for my CLC software?


CLC Genomics Workbench | Am I eligible for support for my CLC software?

In which order to use different tools in CLC Genome Finishing Module?


Workbench Modules

What is myCLC?


CLC Genomics Workbench | Information about myCLC

How can I add someone as a technical contact to myCLC?


CLC Genomics Workbench | Adding a technical contact allows to share information around your licenses

Why is my destination vector not being accepted by the Gateway Cloning tool?


CLC Genomics Workbench

Why are my att sites not recognized by the Gateway Cloning tool?


CLC Genomics Workbench

How are the homozygous and heterozygous calls determined?


CLC Genomics Workbench | This FAQ described when a variants is classified as homozygous or heterozygous

How can I get amino acid prediction information for the variants in my data?


CLC Genomics Workbench | Described the different way of prediction amino acid changes when working with Stand-alone objects or Tracks

How can I analyze and visualize strand specific RNA-Seq data?


CLC Genomics Workbench

What does the error CPU usage limit exceeded mean when I run a search at the NCBI?


CLC Genomics Workbench

Should I run my assembly in stages?


CLC Genomics Workbench | This FAQ described why including all data in one de novo assembly is recommended.

Should I use a masked reference when working with exome or amplicon data?


CLC Genomics Workbench | This FAQ provide background information regarding why it is often not appropriate to use a masked reference for mapping

Why do the CLC Workbenches not import the full chromatogram from AB1 or ABI files?


CLC Genomics Workbench | This FAQ describes why you may not get a full chromatogram from an imported AB1 or ABI file

How can I export the coverage for each position in my mapping?


CLC Genomics Workbench | This FAQ describes how you can export coverage information to a .tsv or .csv file

How can I identify low or zero coverage regions in a mapping?


CLC Genomics Workbench | This FAQ show how to create an annotation track with low coverage regions.

Why do I see a grey box with text saying "Too much data for rendering" when I view a mapping?


CLC Genomics Workbench

How can I see all my reads when viewing high coverage areas of a mapping?


CLC Genomics Workbench

What are the memory requirements for the read mapper?


CLC Genomics Workbench

Can chromosomes downloaded from NCBI be used as a Track-based reference


CLC Genomics Workbench

What does it mean if my host ID field is empty?


CLC Genomics Workbench | What to do if no host ID can be found for a computer a CLC license is downloaded to

How can I find out which machine my license has been downloaded for?


CLC Genomics Workbench | Which computer is using the licenses for the CLC software

What is the host ID for a machine running the CLC License Server software?


CLC Genomics Workbench | How to find the host ID for a computer running CLC License Server

How can I change the decimal notation used by the Workbench


CLC Genomics Workbench | The FAQ show how you can set the Workbench to use dot (.) or a comma (,) as the decimal separator.

What do the navigation area icons mean?


CLC Genomics Workbench | The icons in the navigation area signifies specific data object types. This FAQ list the icons and there meaning.

Why can't I see my license details via myCLC?


CLC Genomics Workbench | Which licenses can be seen in your my CLC account

What is the difference between Tracks and Stand-alone objects?


CLC Genomics Workbench | This FAQ explain the difference between Tracks and Stand-alone objects.

How can I view information for another myCLC account?


CLC Genomics Workbench | Where do I find this information in myCLC

Why are there ambiguity codes and N's in the paired reads of my mapping?


CLC Genomics Workbench | This FAQ describe why ambiguity codes and N's can be present in a read mapping, even that none was present in the un-mapped paired-end reads.

Why do I get contigs shorter than the minimum contig length I specified?


CLC Genomics Workbench

Why is the progress bar stalled/why is the progress bar at 100% but my job is still running?


CLC Genomics Workbench | Description of how to interpret the progress bar.

Should I merge my Overlapping Pairs or not?


CLC Genomics Workbench | Merging of overlapping pairs is generally not recommended in the CLC Workbenches. This FAQ provide information on the things to consider when deciding to merge overlapping pairs or not.

How can I get access to myCLC?


CLC Genomics Workbench | Requesting access to myCLC and resetting the password

How do I save and apply customized View Settings?


CLC Genomics Workbench | To save the view settings in the side panel, so they are applied the next time that you open an object of the same type, please follow the instructions in this FAQ.

How to import predesigned primers to the Workbench?


CLC Genomics Workbench | This FAQ provides instruction on how you can import primers designed using third-party tools into the Workbench.

How can I change the owner of CLC licenses?


CLC Genomics Workbench | How to proceed if you wish to change the owner of CLC licenses

How can I run a batch job with multiple libraries for each sample?


CLC Genomics Workbench

Where can I find manuals and tutorials for CLC software?


CLC Genomics Workbench | Links to the manuals and tutorials of the CLC software

Introduction to IPA Functional Analysis


Overlapping Network


An overview of Overlapping Networks

How can I download a static license file for the Assembly Cell for a non-networked machine?


CLC Assembly Cell | How to download a Assembly Cell license on a system with restricted network access

How can I download a license for the Genomics Server on a non-networked machine?


CLC Genomics Server | Download a CLC Genomics Server license on a machine without external network access

Add BLAST database locations to my CLC Genomics Server


CLC Genomics Server | How can I add BLAST database locations to my Server?

How do I download a network license?


CLC Genomics Workbench | A network license is downloaded to and served by a CLC License Server

Set permissions for BLAST database addition and searching on the CLC Genomics Server


CLC Genomics Server | How can I set permissions for BLAST database addition and searching on the CLC Genomics Server?

How can I upgrade a network license between major versions?


CLC Genomics Workbench | Upgrading network licenses between major versions

How can I download a network license for the CLC License Server running on a non-networked machine?


CLC Genomics Workbench

What do I do with a network license?


CLC Genomics Workbench | How to make use of a network license

How do I download a desktop license for my commercial Workbench plugin or module?


Workbench Modules | Installing and running the commercial plugin/module for the first time or updating from an earlier version

How do I download a desktop license for my Workbench (static license)?


CLC Genomics Workbench | Download a static desktop license for a Workbench

How can I download a static license file for a Workbench being run on a non-networked machine?


CLC Genomics Workbench | Download a static license file for a Workbench without external network access

How can I find out about my licenses?


CLC Genomics Workbench | How to get an overview of your licenses

Network Explorer Tool


Networks View

Analysis Summary Page


Analysis Summary Page

Reviewing Mapped Identifiers


Pathway Filtering


Description of the filters used in Build tools

Metadata keys used in IPA


Description of the existing metadata keys you can use in IPA to annotate your own datasets

Highlight or Select


Overlay tool to identify nodes or relationships in networks and pathways and then act upon them

Highlight


Obsolete, please see Highlight or Select

Core Analysis Setup


Description of how to set up a Core Analysis

Pre-Analysis Filtering


Description of the filters available to pre-filter a Core Analysis

Exporting References


How can I share data with others?


How can I share data with others?

Exporting Images


Cuffdiff file import


Uploading Cuffdiff RNA-Seq files as datasets in IPA

CLC Product FAQs


CLC Genomics Workbench | Please find the link to the CLC product FAQs below.

FAQ


Exploring Upstream Regulators Results in a Pathway


Grow


Function and Disease


Specialized Features index


IPA on Windows


Running IPA on Windows

What are the guidelines for citing IPA in publications?


microRNA Target Filter Workflow


Workflow describing how to use the MicroRNA-Target Filter

Connect


Path Explorer


Path Explorer

Analyzing Genomic Regions from UCSC Genome Browser


How Upstream Regulator Analysis Can Help You


Functional Categories Definitions


Disease or Function View


View/Edit Preferences


Pathway Report


Gene View


ChemView


Mechanistic Networks


Mechanistic Networks

Mechanistic Network Viewer


Export All Analysis Results


Export All

Inhibited phosphoproteins


Overlay Analyses, Datasets, and Lists


Core Analysis Types


Description of the types of Core Analysis types you can run in IPA

Variant gain loss and ACMG classification


Importing and using variant loss/gain and ACMG classification datasets

High Resolution IPA Legend


High Resolution Images of IPA Legend

Batch Analysis


How to run multiple analysis as a batch

Grow to Diseases and Functions


Grow to Diseases and Functions

Comparison analysis heat map for upstream analysis


Comparison analysis heat map for upstream analysis

Molecule Summary


Preview of basic information about a molecule

Layout Options


Choose different ways to arrange nodes on a network or a my pathway

PathTracer


PathTracer

PathTracer


PathTracer

Annotations


Importing Pathways


Collaboration Workspace CWS


Trim and Keep


Add Molecules and Relationships


Advanced Search


Function and Disease Search


Managing Invitations


Molecules


Gene and Chemical Search


Relationships


Pathways and Tox List Search


Shared With Me


Exporting Molecule Lists


Password Reset


Password Reset

Filter Preferences


Canonical Pathway


Gene View, Disease or Function View, Chem View


Gene view Disease or Function view Chem view

Tox Lists


Canonical Pathways for Comparisons


Using Lists


Best Practice - Expression Data Analysis


Creating and Saving My Lists


My Pathway (Tool)


Species Filter


Relationship Types Filter


Biofluids Filter


Tox Functions


Line and Relationship Tool


Tissue and Cell Line Filter


Publication Date Range Filter


Disease Filter


Biomarker Filter


Drug


Background


Text Tool


My List


Path Designer Workflow Overview


Molecules in Path Designer


What can I do with the search results?


What can I do with the search results?

Core, Tox and Metabolomic Analyses


Tox List


Biomarkers


Differences between the search tabs


What’s the difference between the search tabs?

Searching for pathways associated with a gene


How do I search for pathways associated with a gene?

Emailing Interactive Pathways


SNP Content


Compare Data


Compare data tool

Analyzed Dataset


How to Overlay Analyses, Datasets, and Lists

Comparing Biomarkers


How can Functional Analysis help you


IPA-Tox Analysis Overview


Clustering of miRNA in IPA


Printing


Molecule Types Filter


Publication Guidelines


NGS RNA Sequencing


Confidence Level Filter - microRNA


What other tools does IPA work with?


What other tools does IPA work with?

Can I do an analysis with a list of genes only?


Can I do an analysis with a list of genes only?

My Pathways


Overview of MY Pathways

How many genes are up or down regulated in a pathway?


How many genes are up or down regulated in a pathway?

FAQ - microRNA


FAQs on the miRNA targeting relationships in IPA

What kind of data should I have?


What kind of data should I have?

How do I add my own custom genes and connections?


How do I add my own custom genes and connections?

Biomarker Definition


What species identifiers are accepted for analysis by IPA?


What species identifiers are accepted for analysis by IPA?

Downstream Effect Analysis: Evidence for Effect


More info link for Downstream Effect Analysis Evidence for Effect

Upstream Regulator Analysis Evidence for Effect


Can I suggest articles and findings to add?


Can I suggest articles and findings to add?

Creating a Dataset


My file won’t open/upload correctly. What should I do?


My file won’t open/upload correctly. What should I do?

Please select one of the sub categories under Uploading and Analyzing Data


A comprehensive set of feature descriptions is available in the sub categories under Uploading and Analyzing Data. Select the topic you are interested in and the list of available articles will appear in this space.