Genotyping AnnotateSnps.pdf

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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.  
 
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.  
  
[[image:GenotypeAnnoSNP0.png|570x429px]]
+
[[image:SNPannotation.png|570x429px]]
  
 
==General==
 
==General==
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In the "Annotate SNPs" window the user can enter a SNP list by:
 
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 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.
 
* 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===
 
===Options===
  
* Species selection
+
* Species selection / reference genome
* NCBI build selection
+
* Gene annotation / gene model
* Ensembl version
+
* DBSNP version
+
* Server address
+
 
* Output name
 
* Output name
  
  
A table is returned showing annotation information for each SNP, including the Annotation Type and Transcript name, which can be very useful.  
+
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.  
 
+
A table is returned showing annotation information for each SNP, including the Annotation Type  and Transcript name, which can be very useful.
+
  
 
[[image:GenotypeAnnoSNP1.png|707x149px]]
 
[[image:GenotypeAnnoSNP1.png|707x149px]]
 
  
 
==OmicScript==
 
==OmicScript==
 
[[]]
 
[[]]

Revision as of 08:00, 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
  • 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

[[]]