Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • How to read an Affymetrix Axiom genotype (array data) file?

    Hi,

    I'm trying to put together genotype data for wheat samples from this resource:


    The two types of file I get look like this (array probe set):
    Code:
    Affymetrix Code,Bristol Affy Code,Bristol SNP Code,Bristol Contig Code,Sequence (including SNP ambiguity code)
    AX-94381124,BA00222391,No BS code,GJKKTUG01CGTKM_219,...ACGCA[R]ACNTC...
    AX-94381126,BA00232763,No BS code,FZU8VVO01APRT5_148,...TCACT[Y]GNGTG...
    AX-94381127,BA00233916,No BS code,contig77177_250,...CCCGA[M]NCGAC...
    ...
    and (Array data):
    Code:
    A_mutica,A_speltoides,Adhoc,Ae_caudata,Akteur,A...
    AX-94381124,1,-1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,...
    AX-94381126,1,2,2,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2
    AX-94381127,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2...
    ...
    The only other information provided about the files is this explanation:
    0 = AA, 1 = AB, 2 = BB, -1 = No call

    So the question is, what information is required to map from genotype 'score' to actual genotype? Obviously heterozygous calls are clear and distinguished from homozygous calls, but is A. speltoides AA or GG at AX-94381124?

    Are these actually Affymetrix Axiom format files, or just something custom?


    Thanks for help,
    Dan.
    Homepage: Dan Bolser
    MetaBase the database of biological databases.

Latest Articles

Collapse

  • seqadmin
    Exploring the Dynamics of the Tumor Microenvironment
    by seqadmin




    The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
    07-08-2024, 03:19 PM
  • seqadmin
    Exploring Human Diversity Through Large-Scale Omics
    by seqadmin


    In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
    06-25-2024, 06:43 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 07-19-2024, 07:20 AM
0 responses
37 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-16-2024, 05:49 AM
0 responses
47 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-15-2024, 06:53 AM
0 responses
57 views
0 likes
Last Post seqadmin  
Started by seqadmin, 07-10-2024, 07:30 AM
0 responses
43 views
0 likes
Last Post seqadmin  
Working...
X