# General

- [Troubleshooting](/software/general/software-general-troubleshooting-list.md)
- [DRAGEN reference differences for on instrument and standalone analysis](/software/general/software-general-troubleshooting-list/000009589.md)
- [Does the DRAGEN pipeline support VQSR (Variant Quality Score Recalibration)?](/software/general/software-general-troubleshooting-list/000006139.md)
- [How to troubleshoot a "None of the specified endpoints were reachable" error in Local Run Manager](/software/general/software-general-troubleshooting-list/000001217.md)
- [Illumina Connected Analytics (ICA) kernel cannot connect in a Bench Workspaces](/software/general/software-general-troubleshooting-list/000007769.md)
- [Options for demultiplexing libraries with different index lengths in the same sequencing run](/software/general/software-general-troubleshooting-list/000005982.md)
- [Sample specific nucleotide error bias estimation filter and systematic noise filter in DRAGEN](/software/general/software-general-troubleshooting-list/000006989.md)
- [Troubleshooting LRM analysis module not available at run start on NextSeq 500/550](/software/general/software-general-troubleshooting-list/000001904.md)
- [FAQ](/software/general/software-general-faq-list.md)
- [Analysis FAQ for the TruPath Genome assay](/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?](/software/general/software-general-faq-list/000009436.md)
- [How is zygosity assigned for mitochondrial variant calls with DRAGEN?](/software/general/software-general-faq-list/000007537.md)
- [How to invite users to a Project in Illumina Connected Analytics v2](/software/general/software-general-faq-list/000007549.md)
- [How to run the DRAGEN MSI Pipeline](/software/general/software-general-faq-list/000007508.md)
- [How to use the 'OverrideCycles' setting in the Run Planning User Interface](/software/general/software-general-faq-list/000005671.md)
- [Is there a certain number of times that users can requeue local analysis?](/software/general/software-general-faq-list/000007161.md)
- [Why are underscores in sample names changed to dashes in the FASTQ file names?](/software/general/software-general-faq-list/000003636.md)
- [Reference Material](/software/general/software-general-reference_material-list.md)
- [Adapter trimming Why are adapter sequences trimmed from only the 3' ends of reads](/software/general/software-general-reference_material-list/000002905.md)
- [BaseSpace FASTQ Processing Tools for Data Analysis Support Webinar Video](/software/general/software-general-reference_material-list/000008085.md)
- [Creating a custom genome for NovaSeq X Series](/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)](/software/general/software-general-reference_material-list/000005165.md)
- [FASTQ文件解读](/software/general/software-general-reference_material-list/000007412.md)
- [Generating checksums for a file](/software/general/software-general-reference_material-list/000008482.md)
- [Guidelines for reverse complementing i5 sequences for demultiplexing](/software/general/software-general-reference_material-list/000001800.md)
- [How to Add a User to Illumina Connected Multiomics Domain and Workgroup](/software/general/software-general-reference_material-list/000010147.md)
- [How to avoid Ns in small RNA or short reads when running BCL Convert](/software/general/software-general-reference_material-list/000009157.md)
- [How to convert a custom BED file to a manifest file for enrichment analysis](/software/general/software-general-reference_material-list/000002840.md)
- [How to realign a CRAM file to a new reference with DRAGEN](/software/general/software-general-reference_material-list/000007021.md)
- [How to unlock BioSamples in BaseSpace using BaseSpace Command Line Interface (CLI)](/software/general/software-general-reference_material-list/000005845.md)
- [How to use Exome 2.5 Panel of Normals reference for germline deletion/duplication analysis](/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](/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](/software/general/software-general-reference_material-list/000008075.md)
- [Illumina DRAGEN Bio IT Platform Ultra Rapid Analysis of Next Generation Data Support Webinar Video](/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](/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](/software/general/software-general-reference_material-list/000008083.md)
- [Illumina DRAGEN Bio IT Platform What is new with version 3.7 Support Webinar Video](/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](/software/general/software-general-reference_material-list/000008084.md)
- [Illumina DRAGEN v4.0 Unlock the Full Potential of Genomics Support Webinar Video](/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](/software/general/software-general-reference_material-list/000007945.md)
- [Instructions on how to restart run upload to BaseSpace using BaseSpace Broker](/software/general/software-general-reference_material-list/000001811.md)
- [Investigation of Log4j Vulnerability status for Illumina off instrument software products](/software/general/software-general-reference_material-list/000006344.md)
- [Investigation of Log4j Vulnerability with the Illumina DRAGEN Bio IT Platform](/software/general/software-general-reference_material-list/000006340.md)
- [Investigation of Log4j Vulnerability](/software/general/software-general-reference_material-list/000006335.md)
- [Maximum number of cycles for index reads on the NovaSeq X Series](/software/general/software-general-reference_material-list/000008417.md)
- [Metagenomic Sequencing Introduction to Data Analysis Support Webinar Video](/software/general/software-general-reference_material-list/000007979.md)
- [NextSeq 1000/2000 Introduction to Analysis with DRAGEN Support Webinar Video](/software/general/software-general-reference_material-list/000008076.md)
- [Sequencing Data Analysis Introduction to Key Concepts Support Webinar Video](/software/general/software-general-reference_material-list/000007978.md)
- [Trimming T overhang options for Illumina Stranded mRNA and Illumina Stranded Total RNA workflows](/software/general/software-general-reference_material-list/000003227.md)
- [TruSight Oncology 500 Assays and Analysis Options](/software/general/software-general-reference_material-list/000003812.md)
- [Upgrading from bcl2fastq to BCL Convert](/software/general/software-general-reference_material-list/000003710.md)
- [Using an N wildcard in index sequences in different Illumina FASTQ generation software](/software/general/software-general-reference_material-list/000003560.md)
- [Which orientation are the indexes in Top\_Unknown\_Barcodes output from BclConvert?](/software/general/software-general-reference_material-list/000005078.md)
- [Why is allowing mismatches when demultiplexing desirable?](/software/general/software-general-reference_material-list/000007484.md)