Genotyping AnnotateSnps.pdf

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* Species selection / reference genome
 
* Species selection / reference genome
 
* Gene annotation / gene model
 
* Gene annotation / gene model
 +
Please note that OmicSoft does not maintain every combination of reference genome and gene model as this procedure was replaced by GeneticsLand. <br />
 +
Contact OmicSoft Support if you would like more information about GeneticsLands. <br />
 +
 +
The proc uses files that are here: http://omicsoft.com/downloads/genomebrowser/tables/
 +
If the file does not exist at the above link then you will receive an Object Reference Error.
 
* Output name
 
* Output name
  

Latest revision as of 08:04, 30 June 2020

Contents

SNP Annotations

Array Studio will use Omicsoft’s Array Server to retrieve SNP Annotation information for a user provided list of SNP identifiers (an internet connection is required). The first time this command is used it may take a while longer to load.

SNPannotation.png

General

SNP List

In the "Annotate SNPs" window the user can enter a SNP list by:

  • Copy/Paste - Copy list or rsIDs into white space of menu options.
  • Load from solution - Allows user to select an existing SNP list from the Solution Explorer.
  • Load from file - Allows user to select an existing text file on their computer.

Please note that the procedure only supports SNP identifies such as rsID. You cannot enter chr:position for your SNP identifier.

Options

  • Species selection / reference genome
  • Gene annotation / gene model

Please note that OmicSoft does not maintain every combination of reference genome and gene model as this procedure was replaced by GeneticsLand.
Contact OmicSoft Support if you would like more information about GeneticsLands.

The proc uses files that are here: http://omicsoft.com/downloads/genomebrowser/tables/ If the file does not exist at the above link then you will receive an Object Reference Error.

  • Output name


A table is returned showing chromosome, position, reference, and alternative alleles for each SNP, including the Annotation Type (intron, exon-coding, 3'UTR, etc.) Transcript ID, and AA Position / AAChange / AAFrame, if pertinent.

GenotypeAnnoSNP1.png

OmicScript

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