Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • illumina raw genotype data format

    Hello,

    I was wondering if anyone could help me out with understanding the format or share links where I could infer the genotype data produced from Genome Studio Illumina 2.5 export.

    I wish to know the meaning mainly for "Allele1 - Forward" "Allele2 - Forward" "Allele1 - Top" "Allele2 - Top" "Allele1 - Design" "Allele2 - Design" "Allele1 - AB" "Allele2 - AB" .

    Your help is appreciated.

    Thank you.

  • #2
    Resurrecting an old post here, but I need help with a related issue. Illumina have a note describing their system for genotype calling from array data



    My problem is that I have genotypes from an illumina cyto12 genotyping array and exome SNP calls from the same samples (human). I would like to assess how well the genotypes match (or not) but I am stuck trying to get the illumina array genotypes to correspond to the human reference sequence strand - as used by GATK.

    Any suggestions? - currently I am limited to comparing zygosity between the two methods (homozygous AA, BB; or heterozygous AB), but would really like to compare alleles called by both methods.

    Thanks

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 03-27-2024, 06:37 PM
    0 responses
    12 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-27-2024, 06:07 PM
    0 responses
    11 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    52 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    68 views
    0 likes
    Last Post seqadmin  
    Working...
    X