# Software - [General](https://knowledge.illumina.com/software/general.md) - [Troubleshooting](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list.md) - [DRAGEN reference differences for on instrument and standalone analysis](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000009589.md) - [Does the DRAGEN pipeline support VQSR (Variant Quality Score Recalibration)?](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000006139.md) - [How to troubleshoot a "None of the specified endpoints were reachable" error in Local Run Manager](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000001217.md) - [Illumina Connected Analytics (ICA) kernel cannot connect in a Bench Workspaces](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000007769.md) - [Options for demultiplexing libraries with different index lengths in the same sequencing run](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000005982.md) - [Sample specific nucleotide error bias estimation filter and systematic noise filter in DRAGEN](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000006989.md) - [Troubleshooting LRM analysis module not available at run start on NextSeq 500/550](https://knowledge.illumina.com/software/general/software-general-troubleshooting-list/000001904.md) - [FAQ](https://knowledge.illumina.com/software/general/software-general-faq-list.md) - [Analysis FAQ for the TruPath Genome assay](https://knowledge.illumina.com/software/general/software-general-faq-list/000010170.md) - [Does TruSight Oncology 500 (TSO500) use a segmentation algorithm to determine the genomic coordinates of a copy number call?](https://knowledge.illumina.com/software/general/software-general-faq-list/000009436.md) - [How is zygosity assigned for mitochondrial variant calls with DRAGEN?](https://knowledge.illumina.com/software/general/software-general-faq-list/000007537.md) - [How to invite users to a Project in Illumina Connected Analytics v2](https://knowledge.illumina.com/software/general/software-general-faq-list/000007549.md) - [How to run the DRAGEN MSI Pipeline](https://knowledge.illumina.com/software/general/software-general-faq-list/000007508.md) - [How to use the 'OverrideCycles' setting in the Run Planning User Interface](https://knowledge.illumina.com/software/general/software-general-faq-list/000005671.md) - [Is there a certain number of times that users can requeue local analysis?](https://knowledge.illumina.com/software/general/software-general-faq-list/000007161.md) - [Why are underscores in sample names changed to dashes in the FASTQ file names?](https://knowledge.illumina.com/software/general/software-general-faq-list/000003636.md) - [Reference Material](https://knowledge.illumina.com/software/general/software-general-reference_material-list.md) - [Adapter trimming Why are adapter sequences trimmed from only the 3' ends of reads](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000002905.md) - [BaseSpace FASTQ Processing Tools for Data Analysis Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008085.md) - [Creating a custom genome for NovaSeq X Series](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000009590.md) - [Different options/apps/pipelines available on the MiSeq i100, Nextseq2000, NovaSeqX, DRAGEN on BaseSpace, DRAGEN server and on Illumina Connected Analytics (ICA)](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000005165.md) - [FASTQ文件解读](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000007412.md) - [Generating checksums for a file](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008482.md) - [Guidelines for reverse complementing i5 sequences for demultiplexing](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000001800.md) - [How to Add a User to Illumina Connected Multiomics Domain and Workgroup](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000010147.md) - [How to avoid Ns in small RNA or short reads when running BCL Convert](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000009157.md) - [How to convert a custom BED file to a manifest file for enrichment analysis](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000002840.md) - [How to realign a CRAM file to a new reference with DRAGEN](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000007021.md) - [How to unlock BioSamples in BaseSpace using BaseSpace Command Line Interface (CLI)](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000005845.md) - [How to use Exome 2.5 Panel of Normals reference for germline deletion/duplication analysis](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000007918.md) - [Illumina DRAGEN Bio IT Platform What is new with version 3.10 updates Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008073.md) - [Illumina DRAGEN Bio IT Platform What is new with version 3.9 updates Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008075.md) - [Illumina DRAGEN Bio IT Platform Ultra Rapid Analysis of Next Generation Data Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008091.md) - [Illumina DRAGEN Bio IT Platform What is new with version 3.5 updates Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008088.md) - [Illumina DRAGEN Bio IT Platform What is new with version 3.6 updates Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008083.md) - [Illumina DRAGEN Bio IT Platform What is new with version 3.7 Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008086.md) - [Illumina DRAGEN Bio IT Platform What is new with version 3.8 updates Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008084.md) - [Illumina DRAGEN v4.0 Unlock the Full Potential of Genomics Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008072.md) - [Information on leading r for UMIs when demultiplexing NextSeq 1000/2000 or NovaSeq X series data with BCL Convert](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000007945.md) - [Instructions on how to restart run upload to BaseSpace using BaseSpace Broker](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000001811.md) - [Investigation of Log4j Vulnerability status for Illumina off instrument software products](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000006344.md) - [Investigation of Log4j Vulnerability with the Illumina DRAGEN Bio IT Platform](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000006340.md) - [Investigation of Log4j Vulnerability](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000006335.md) - [Maximum number of cycles for index reads on the NovaSeq X Series](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008417.md) - [Metagenomic Sequencing Introduction to Data Analysis Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000007979.md) - [NextSeq 1000/2000 Introduction to Analysis with DRAGEN Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000008076.md) - [Sequencing Data Analysis Introduction to Key Concepts Support Webinar Video](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000007978.md) - [Trimming T overhang options for Illumina Stranded mRNA and Illumina Stranded Total RNA workflows](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000003227.md) - [TruSight Oncology 500 Assays and Analysis Options](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000003812.md) - [Upgrading from bcl2fastq to BCL Convert](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000003710.md) - [Using an N wildcard in index sequences in different Illumina FASTQ generation software](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000003560.md) - [Which orientation are the indexes in Top\_Unknown\_Barcodes output from BclConvert?](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000005078.md) - [Why is allowing mismatches when demultiplexing desirable?](https://knowledge.illumina.com/software/general/software-general-reference_material-list/000007484.md) - [3rd Party Software](https://knowledge.illumina.com/software/3rd-party-software.md) - [Reference Material](https://knowledge.illumina.com/software/3rd-party-software/software-3rd-party-software-reference_material-list.md) - [How to upload files to Illumina Kiteworks using command line tools](https://knowledge.illumina.com/software/3rd-party-software/software-3rd-party-software-reference_material-list/000009128.md) - [FAQ](https://knowledge.illumina.com/software/3rd-party-software/software-3rd-party-software-faq-list.md) - [Information Regarding OpenSSL v3 Vulnerability](https://knowledge.illumina.com/software/3rd-party-software/software-3rd-party-software-faq-list/000007171.md) - [BaseSpace CLI](https://knowledge.illumina.com/software/basespace-cli.md) - [Troubleshooting](https://knowledge.illumina.com/software/basespace-cli/software-basespace-cli-troubleshooting-list.md) - [BaseSpace Command Line Interface upload failure with request signature error](https://knowledge.illumina.com/software/basespace-cli/software-basespace-cli-troubleshooting-list/000007037.md) - [Resolving Basespace CLI analysis launch error Resource FileSummary doesn't exist](https://knowledge.illumina.com/software/basespace-cli/software-basespace-cli-troubleshooting-list/000010173.md) - [Troubleshooting "Permission denied" error when attempting to run BaseSpace CLI on Linux and Mac OS](https://knowledge.illumina.com/software/basespace-cli/software-basespace-cli-troubleshooting-list/000003380.md) - [Reference Material](https://knowledge.illumina.com/software/basespace-cli/software-basespace-cli-reference_material-list.md) - [Bulk Deletion of Runs and Projects Using BaseSpace CLI with Windows PowerShell](https://knowledge.illumina.com/software/basespace-cli/software-basespace-cli-reference_material-list/000010078.md) - [How to authenticate BaseSpace CLI to workgroup](https://knowledge.illumina.com/software/basespace-cli/software-basespace-cli-reference_material-list/000008347.md) - [How to upload and download FASTQ files to BaseSpace with BaseSpace CLI](https://knowledge.illumina.com/software/basespace-cli/software-basespace-cli-reference_material-list/000001138.md) - [BaseSpace Sequence Hub](https://knowledge.illumina.com/software/basespace-sequence-hub.md) - [Reference Material](https://knowledge.illumina.com/software/basespace-sequence-hub/software-basespace-sequence-hub-reference_material-list.md) - [How to accept BaseSpace transfer ownership requests in a workgroup context](https://knowledge.illumina.com/software/basespace-sequence-hub/software-basespace-sequence-hub-reference_material-list/000009086.md) - [How to change ownership of a BaseSpace Professional Workgroup or Enterprise Domain](https://knowledge.illumina.com/software/basespace-sequence-hub/software-basespace-sequence-hub-reference_material-list/000007942.md) - [How to share BaseSpace Sequence Hub sequencing data from enterprise domain to public domain](https://knowledge.illumina.com/software/basespace-sequence-hub/software-basespace-sequence-hub-reference_material-list/000001666.md) - [How to transfer data in BaseSpace from Public Domain to Enterprise Domain](https://knowledge.illumina.com/software/basespace-sequence-hub/software-basespace-sequence-hub-reference_material-list/000003654.md) - [BclConvert bcl2fastq](https://knowledge.illumina.com/software/bclconvert-bcl2fastq.md) - [Reference Material](https://knowledge.illumina.com/software/bclconvert-bcl2fastq/software-bclconvert-bcl2fastq-reference_material-list.md) - [How to set OverrideCycles values for variable index sequence lengths on the NovaSeq X/X Plus](https://knowledge.illumina.com/software/bclconvert-bcl2fastq/software-bclconvert-bcl2fastq-reference_material-list/000008935.md) - [Troubleshooting](https://knowledge.illumina.com/software/bclconvert-bcl2fastq/software-bclconvert-bcl2fastq-troubleshooting-list.md) - [Troubleshooting BCLConvert showing Read 1 Cycles 0 and QC Status Failed](https://knowledge.illumina.com/software/bclconvert-bcl2fastq/software-bclconvert-bcl2fastq-troubleshooting-list/000009654.md) - [Cloud Software](https://knowledge.illumina.com/software/cloud-software.md) - [Reference Material](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list.md) - [BaseSpace Command Line Tools for Basic Analysis Part I Support Webinar Video](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000008080.md) - [BaseSpace Command Line Tools for Basic Analysis Part II Support Webinar Video](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000008082.md) - [BaseSpace Data Model Explained](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000007009.md) - [BaseSpace Informatics Suite Intro to Cohort Analyzer and Correlation Engine Support Webinar Video](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000008089.md) - [BaseSpace Sequence Hub Introduction and Analysis Overview Support Webinar Video](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000008087.md) - [BaseSpace Sequence Hub informational resources](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000002876.md) - [DRAGEN Enrichment App in BaseSpace](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000003686.md) - [DRAGEN Metagenomics Pipeline in BaseSpace general information](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000003688.md) - [Enrichment Data Analysis Introduction Support Webinar Video](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000008090.md) - [How to Analyze Data using BaseSpace DRAGEN COVID Lineage App Video](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000006961.md) - [How to Requeue Analysis for a NextSeq 1000/2000 run using BaseSpace BCL Convert Video](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000006955.md) - [How to Requeue a Run using BaseSpace Sequence Hub Video](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000006956.md) - [How to authenticate BaseSpace CLI to another region or Enterprise domain](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000005560.md) - [How to concatenate the FASTQ files from different lanes](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000002035.md) - [How to configure Single Sign On (SSO) for an Illumina Enterprise domain using Entra ID](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000005972.md) - [How to configure Single Sign On (SSO) for an Illumina Enterprise domain using Okta](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000006210.md) - [How to delete a variant with API in Emedgene Curate](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000009725.md) - [How to download FASTQs from specific lanes using Basespace CLI](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000006973.md) - [How to download only FASTQs from a BaseSpace project using BaseSpace CLI](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000003376.md) - [How to download specific file types when downloading runs from BaseSpace using BaseSpace CLI](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000003154.md) - [How to edit a sample sheet and requeue an analysis in BaseSpace Sequence Hub](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000001321.md) - [How to find the Demultiplexing Summary and SampleSheetUsed in BaseSpace?](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000003652.md) - [How to get started with BaseSpace Command Line Interface (CLI) Video](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000005593.md) - [How to import files into a BaseSpace Project using the web Interface](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000003651.md) - [How to install the BaseSpace Sequence Hub Downloader on Mac OS](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000003049.md) - [How to invite users to an Enterprise domain workgroup, via a collaborative Enterprise domain account](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000005878.md) - [How to launch any app in BaseSpace using BaseSpace Command Line Interface (CLI)](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000007759.md) - [How to launch the DRAGEN COVID Lineage app using BaseSpace CLI?](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000005230.md) - [How to list BaseSpace entities using BaseSpace CLI](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000003682.md) - [How to manage status.illumina.com subscriptions](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000009049.md) - [How to requeue (re launch) the autolaunch analysis on BaseSpace](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000008562.md) - [How to set the default location for uploaded runs to BaseSpace](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000001847.md) - [How to share BaseSpace sequencing runs and project data using 'Get Link' option](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000001597.md) - [How to unlock a Biosample in BaseSpace that is locked due to Biosample Data Aggregation](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000003653.md) - [How to upload a run to BaseSpace using BaseSpace Command Line Interface (CLI)](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000003298.md) - [How to use the DRAGEN TSO500 v1.1/DRAGEN TSO500 ctDNA v1.2 pipelines on ICA using FASTQ files](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000007098.md) - [How to use the Resources page to add custom reference files for Run Planning for NovaSeq X/X Plus runs](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000008500.md) - [Instructions for using BaseSpace CLI on Windows to upload runs](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000007950.md) - [Investigation of Log4j Vulnerability with BaseSpace Sequence Hub (BSSH) Cloud](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000006337.md) - [Investigation of Log4j Vulnerability with Illumina Connected Analytics (ICA)](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000006343.md) - [Investigation of Log4j Vulnerability with TruSight Software Suite (TSS)](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000006341.md) - [Panel of Normals TruSight Hereditary Cancer Panel datasets for copy number variations in BaseSpace](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000007929.md) - [RNA Sequencing Part III Introduction to Analysis Support Webinar Video](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000008079.md) - [Reference genome and target regions BED file for the DRAGEN PopGen app](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000007889.md) - [Transferring data between a personal account and a Professional workgroup in BaseSpace Sequence Hub](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000001798.md) - [TruSight Oncology 500 version 2 Analysis Overview Support Webinar Video](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000008077.md) - [Uploading Runs BaseSpace Command Line Interface (CLI) Video](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000005857.md) - [Uploading and downloading FASTQ files with BaseSpace CLI Video](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000005860.md) - [What is restricted when a BaseSpace Basic user exceeds 1TB storage limit](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000005662.md) - [Which BaseSpace Subscription is needed to process Illumina 3' Single Cell RNA Samples](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000009794.md) - [Which BaseSpace apps and features use Illumina Connected Analytics](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000009045.md) - [使用BaseSpace基因云计算平台和bcl2fastq2 2.17以及以上版本软件时，如何排查拆分异常情况](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-reference_material-list/000007134.md) - [Troubleshooting](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list.md) - [BaseSpace and Proactive outage resource page](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list/000007381.md) - [DRAGEN Imputation App v 4.0.3 on BaseSpace](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list/000007061.md) - [Details about DRAGEN Metagenomics Kraken2 Database](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list/000008424.md) - [Emedgene troubleshooting information request form](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list/000008955.md) - [How to demultiplex mixed libraries on the same lane in BaseSpace](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list/000002853.md) - [How to download files needed for Sequencing Analysis Viewer from BaseSpace using BaseSpace CLI](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list/000006942.md) - [How to recover a BaseSpace password reset email](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list/000003658.md) - [How to restart Universal Copy Service when a run is stuck uploading to BaseSpace Sequence Hub](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list/000001808.md) - [How to review bsshoutput.json to assess BaseSpace file project mapping from Instrument Autolaunch Analysis](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list/000008916.md) - [Requirements for uploading FASTQ Files to BaseSpace via web interface](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list/000001313.md) - [Troubleshooting "Failed to validate certificate" error when launching IGV BaseSpace Application](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list/000007890.md) - [Troubleshooting DRAGEN analysis error UMI processing is enabled but QNAME does not have UMI section](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list/000008107.md) - [Troubleshooting DRAGEN single cell RNA App UMI error in BaseSpace](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list/000009852.md) - [Troubleshooting Illumina Service Connector not connected for Window computer](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list/000008566.md) - [Troubleshooting demultiplexing issues using BaseSpace Sequence Hub and bcl2fastq2 v2.17+](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list/000002875.md) - [Troubleshooting emptying the trash in BaseSpace Sequence Hub](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list/000007563.md) - [Understanding how instrument autolaunch analysis maps to BaseSpace projects](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list/000008915.md) - [What to do if a BaseSpace analysis is stuck or stalled running](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list/000007380.md) - [Why an appsession API call may only returning a subset of datasets from BaseSpace](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-troubleshooting-list/000007567.md) - [FAQ](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-faq-list.md) - [Are the files for SAV available from BaseSpace if the run was performed with only Run Monitoring?](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-faq-list/000007165.md) - [BaseSpace Sequence Hub archival storage FAQs](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-faq-list/000005875.md) - [BaseSpace v7.12 update frequently asked questions](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-faq-list/000007948.md) - [Can BaseSpace files be transferred directly to AWS (Amazon Web Services)?](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-faq-list/000002832.md) - [Coverage and frequency requirements for variants in FASTA output from the DRAGEN COVID Lineage app](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-faq-list/000005335.md) - [Different coverage reports from the DRAGEN Enrichment analysis](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-faq-list/000006992.md) - 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[How to transfer runs/datasets between different regional servers using BaseSpace CLI](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-faq-list/000005682.md) - [How to use a custom virus primer BED file with the DRAGEN COVID Lineage app on BaseSpace](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-faq-list/000006251.md) - [How to use an API call to download FastQ files from BaseSpace](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-faq-list/000007506.md) - [How to view files from Illumina Connected Analytics in Integrative Genomics Viewer](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-faq-list/000007465.md) - [Is there a limit to the number of files that can be stored within an ICA project?](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-faq-list/000009959.md) - [Running DRAGEN Amplicon 3.10.4 on BaseSpace on a single sample type with a hg38 reference](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-faq-list/000007870.md) - [What are the different BaseSpace Account Types?](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-faq-list/000002846.md) - [What is the BaseSpace data deletion policy?](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-faq-list/000002847.md) - [What is the process for renewing a BaseSpace Professional Workgroup account?](https://knowledge.illumina.com/software/cloud-software/software-cloud-software-faq-list/000006724.md) - [Control Software](https://knowledge.illumina.com/software/control-software.md) - [Troubleshooting](https://knowledge.illumina.com/software/control-software/software-control-software-troubleshooting-list.md) - [Troubleshooting "the owner of workgroup does not have access to the workgroup" message in BaseSpace](https://knowledge.illumina.com/software/control-software/software-control-software-troubleshooting-list/000009510.md) - [DRAGEN](https://knowledge.illumina.com/software/dragen.md) - [FAQ](https://knowledge.illumina.com/software/dragen/software-dragen-faq-list.md) - 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[Creating custom reference genomes (non human) to use with DRAGEN apps on BaseSpace Sequence Hub](https://knowledge.illumina.com/software/dragen/software-dragen-troubleshooting-list/000007488.md) - [Instructions to back up DRAGEN license files when upgrading the operating system on a DRAGEN server](https://knowledge.illumina.com/software/dragen/software-dragen-troubleshooting-list/000008620.md) - [Illumina Connected Analytics (ICA)](https://knowledge.illumina.com/software/illumina-connected-analytics-ica.md) - [Reference Material](https://knowledge.illumina.com/software/illumina-connected-analytics-ica/software-illumina-connected-analytics-_op_ica_cp_-reference_material-list.md) - [How to install an Illumina Connected Analytics service connector on Linux Video](https://knowledge.illumina.com/software/illumina-connected-analytics-ica/software-illumina-connected-analytics-_op_ica_cp_-reference_material-list/000006954.md) - [Where data copied from BaseSpace to ICA are stored on ICA](https://knowledge.illumina.com/software/illumina-connected-analytics-ica/software-illumina-connected-analytics-_op_ica_cp_-reference_material-list/000008546.md) - [Troubleshooting](https://knowledge.illumina.com/software/illumina-connected-analytics-ica/software-illumina-connected-analytics-_op_ica_cp_-troubleshooting-list.md) - [Troubleshooting aborted ICA v2 analyses on BaseSpace](https://knowledge.illumina.com/software/illumina-connected-analytics-ica/software-illumina-connected-analytics-_op_ica_cp_-troubleshooting-list/000008907.md) - [Illumina Connected Multiomics (ICM)](https://knowledge.illumina.com/software/illumina-connected-multiomics-icm.md) - [FAQ](https://knowledge.illumina.com/software/illumina-connected-multiomics-icm/software-illumina-connected-multiomics-_op_icm_cp_-faq-list.md) - [How to check what version of Illumina Connected Multiomics is released](https://knowledge.illumina.com/software/illumina-connected-multiomics-icm/software-illumina-connected-multiomics-_op_icm_cp_-faq-list/000010047.md) - [Reference Material](https://knowledge.illumina.com/software/illumina-connected-multiomics-icm/software-illumina-connected-multiomics-_op_icm_cp_-reference_material-list.md) - [How to Access and Share Illumina Connected Multiomics (ICM) Analysis Logs](https://knowledge.illumina.com/software/illumina-connected-multiomics-icm/software-illumina-connected-multiomics-_op_icm_cp_-reference_material-list/000010048.md) - [How to import Demo Data into Illumina Connected Multiomics](https://knowledge.illumina.com/software/illumina-connected-multiomics-icm/software-illumina-connected-multiomics-_op_icm_cp_-reference_material-list/000010107.md) - [How to optimize ICM (Illumina Connected Multiomics) Data Viewer Performance](https://knowledge.illumina.com/software/illumina-connected-multiomics-icm/software-illumina-connected-multiomics-_op_icm_cp_-reference_material-list/000010030.md) - [Importing raw Single Cell RNA Data into Illumina Connected Multiomics](https://knowledge.illumina.com/software/illumina-connected-multiomics-icm/software-illumina-connected-multiomics-_op_icm_cp_-reference_material-list/000010024.md) - [On Instrument Analysis Software](https://knowledge.illumina.com/software/on-instrument-analysis-software.md) - [Reference Material](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list.md) - [Allowed characters for Run Names and Sample IDs in Local Run Manager v3](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000005750.md) - [Comparison of MiSeq Reporter and Local Run Manager analysis workflows](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000005974.md) - [Connecting remotely to Local Run Manager v4 on instrument](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000002323.md) - [How to Specify Adapters for Trimming in Local Run Manager](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000003678.md) - [How to add a Custom Reference Genome in Local Run Manager](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000002685.md) - [How to generate FASTQ files for index reads in MiSeq Reporter](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000001326.md) - [How to generate FASTQ files from an incomplete run in MiSeq Reporter](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000001325.md) - [How to requeue analysis of a run with MiSeq Reporter](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000001782.md) - [How to set up an AmpliSeq for Illumina run using Local Run Manager v1.3 for MiniSeq](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000002952.md) - [How to use a custom library prep kit in Local Run Manager v2](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000001317.md) - [How to use custom library prep and index kits with Local Run Manager v3 and v4](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000005897.md) - [Local Run Manager How to create FASTQ files for index reads](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000001323.md) - [Local Run Manager v3 with MiSeq Control Software v4 Introduction Support Webinar Video](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000008078.md) - [Local Run Manager 如何利用不完整的测序结果生成FASTQ文件](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000007112.md) - [Using Illumina Experiment Manager (IEM) to Create a Sample Sheet for Illumina Libraries Video](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000005856.md) - [如何使MiSeq Reporter生成Index Reads 的FASTQ文件](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000007352.md) - [如何使用MiSeq Reporter从未完成的run中创建出FASTQ文件](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000007401.md) - [如何使用MiSeq Reporter重新分析一个run？](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000007342.md) - [如何在Local Run Manage中进行重分析（Requeue）及导入运行数据（Import）再分析](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000007141.md) - [如何将桌面测序仪和Local Run Manager与网络存储位置进行连接](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-reference_material-list/000007367.md) - [FAQ](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-faq-list.md) - [Can a run be started on the NovaSeq X/X Plus while an analysis is ongoing?](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-faq-list/000008267.md) - [Can the MiSeq System generate FASTQ files?](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-faq-list/000002606.md) - [MiSeq Reporter Common Questions](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-faq-list/000002240.md) - [Troubleshooting](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list.md) - 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[Troubleshooting demultiplexing issues using onboard DRAGEN on the NextSeq 1000/2000](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000003817.md) - [Unlocking an account or resetting the password on Local Run Manager version 4](https://knowledge.illumina.com/software/on-instrument-analysis-software/software-on-instrument-analysis-software-troubleshooting-list/000009008.md) - [On Premises Software](https://knowledge.illumina.com/software/on-premises-software.md) - [Troubleshooting](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-troubleshooting-list.md) - [BCL Convert software output files](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-troubleshooting-list/000005979.md) - [Cannot specify ' with failed reads' with cbcl input data." error in bcl2fastq2](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-troubleshooting-list/000003571.md) - 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[How to demultiplex an incomplete run using bcl2fastq2 and BCL Convert](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-troubleshooting-list/000003577.md) - [How to troubleshoot barcode collision and not enough hamming distance errors when demultiplexing runs with BCL Convert and bcl2fastq2](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-troubleshooting-list/000002326.md) - [Reference Material](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list.md) - [BCL Convert and index UMIs How to demultiplex samples and output a UMI FASTQ](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list/000007337.md) - [Bcl2Fastq v2+Introduction Support Webinar Video](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list/000008093.md) - [Considerations for using a DRAGEN Server with an automated job scheduler](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list/000001821.md) - [DRAGEN TSO500 Analysis on Illumina Connected Analytics Video](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list/000007125.md) - [DRAGEN TruSight Oncology 500 (TSO500) co install options](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list/000009369.md) - [How to add a custom library prep kit to Illumina Experiment Manager](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list/000002346.md) - [How to create a Project connector in Illumina Connected Analytics Video](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list/000006953.md) - [How to demultiplex a run without using either the i7 index or the i5 index using bcl2fastq2](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list/000003145.md) - [How to demultiplex a sequencing run without using either the i7 or the i5 index using BCL Convert](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list/000005166.md) - [How to demultiplex multiple library types on the same run with multiple lanes using bcl2fastq2](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list/000003578.md) - [How to install an Illumina Connected Analytics service connector on Windows Video](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list/000006952.md) - [How to install an Illumina Connected Analytics service connector on macOS Video](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list/000007123.md) - [How to parse the Counts sparse matrix file output by the DRAGEN scRNA and scATAC pipelines](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list/000007911.md) - [How to update the DRAGEN BIOS version to reduce v4 server fan noise](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list/000009378.md) - [Information on BCL Convert software releases](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list/000009158.md) - [Investigation of Log4j Vulnerability with Emedgene](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list/000006338.md) - [Labeled components of a v1 sample sheet](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list/000002204.md) - [Recommendation to abort ongoing DRAGEN analysis](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list/000008557.md) - [Running DRAGEN analyses with ORA files as input](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-reference_material-list/000007955.md) - [FAQ](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-faq-list.md) - [Can a 10 Gbps connection support data analysis between the DRAGEN server and storage server?](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-faq-list/000006042.md) - [How to avoid Ns in small RNA reads or short reads after running bcl2fastq2?](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-faq-list/000003147.md) - [How to calculate the DRAGEN license quota](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-faq-list/000005077.md) - [How to cold boot or power cycle a DRAGEN server?](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-faq-list/000005673.md) - [How to find the FPGA serial number on a DRAGEN server?](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-faq-list/000009166.md) - [How to generate FASTQs for a run without specifying indexes using BCL Convert](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-faq-list/000007493.md) - [How to output both gVCF and VCF in a single DRAGEN run?](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-faq-list/000007869.md) - [How to use a custom cross contamination VCF file with DRAGEN](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-faq-list/000007495.md) - [Visualizing the DRAGEN Evidence BAM in Integrative Genomics Viewer (IGV)](https://knowledge.illumina.com/software/on-premises-software/software-on-premises-software-faq-list/000007836.md) - [Partek Flow](https://knowledge.illumina.com/software/partek-flow.md) - [Reference Material](https://knowledge.illumina.com/software/partek-flow/software-partek-flow-reference_material-list.md) - [How to add Illumina support as collaborators to projects in Partek Flow](https://knowledge.illumina.com/software/partek-flow/software-partek-flow-reference_material-list/000009718.md) - [TSO500 TST170](https://knowledge.illumina.com/software/tso500-tst170.md) - [Reference Material](https://knowledge.illumina.com/software/tso500-tst170/software-tso500-tst170-reference_material-list.md) - [Information on controls used in TruSight Oncology 500 demo datasets](https://knowledge.illumina.com/software/tso500-tst170/software-tso500-tst170-reference_material-list/000010057.md) - [FAQ](https://knowledge.illumina.com/software/tso500-tst170/software-tso500-tst170-faq-list.md) - [Sample Sheet templates for TruSight Oncology 500 v2 (TSO500 v2)](https://knowledge.illumina.com/software/tso500-tst170/software-tso500-tst170-faq-list/000009750.md) --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. 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