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Exome workflow with analysis in ArrayStar
SeqMan NGen Tutorials » Exome workflow with analysis in ArrayStar
The following video shows how to set up an exome assembly and illustrates downstream analysis in ArrayStar. No data files are provided for this tutorial.
Use the DNASTAR Cloud Data Drive
Use the DNASTAR Cloud Data Drive
The DNASTAR Cloud Data Drive works as both a Cloud file browser and a mechanism for transferring data between your desktop/laptop computer and the DNASTAR Cloud. Your data and results are stored in a private, encrypted Amazon Web Services (AWS) account visible only to…
Add sequences from your computer or the cloud
Add and remove files in the wizard » Add sequences from your computer or the cloud
Some wizard screens require you to add at least one sequence or genome template before proceeding. In these cases, the “Next” button only appears after the item has been added. To add one or more sequences from your computer (i.e. “local”…
De novo assembly using Sanger data
SeqMan NGen Tutorials » De novo assembly using Sanger data
In this tutorial, you will de novo assemble fourteen short trace sequences from PE Applied Biosystems, Inc. and then analyze the resulting contig in SeqMan Ultra. Scroll to the bottom of this topic for a short video showing a slightly different version of this tutorial…
Part B: Finding a putative duplication in the reference sequence using ArrayStar
SeqMan NGen Tutorials » Copy number variation (CNV) workflow with analysis in ArrayStar and GenVision Pro » Part B: Finding a putative duplication in the reference sequence using ArrayStar
In Part A of this tutorial, you ran an assembly and launched the results in ArrayStar. In this part, you will use the ArrayStar Gene Table to locate potential duplications in the reference sequence. Imagine that you would like to find a region that is repeated in the…
Make a custom BED file
Wizard screen descriptions » Input Reference (Sequence, Genome, for Scaffolding, etc.) » Specify a VCF, BED or Manifest file » Make a custom BED file
Certain workflows allow or require you to import a targeted regions file, also known as a BED file, within the Reference Sequence screen. BED files are used to define capture regions in the assembly, and can be generated by the sequence provider or made by hand. These…
Add a genome template from DNASTAR
Add and remove files in the wizard » Add a genome template from DNASTAR
If your workflow includes the Reference Sequence or Set Contaminant screen, you must add at least one reference sequence, biome genome, or genome template before proceeding. Curated and up-to-date DNASTAR genome template packages are available for common model…
Make a custom VCF file
Wizard screen descriptions » Input Reference (Sequence, Genome, for Scaffolding, etc.) » Specify a VCF, BED or Manifest file » Make a custom VCF file
Variant Call Format (VCF) files have multiple uses. For instance, they can provide a way to flag previously known SNPs and to filter them in SNP tables. In DNASTAR’s SeqMan NGen, these SNPs are called "annotated SNPs"; in ArrayStar, they are referred to as "user…