Golden Helix Newsletter

 
Turning SRA Files Into Usable BAMs and VCFs
by Andrew Jesaitis, Product Manager

Turning SRA Files Into Usable BAMs and VCFs
In our recent webcast, Advancing Agrigenomic Discoveries with Sequencing and GWAS Research, Greta Linse Peterson featured bovine data which she download from the NCBI website. The data was downloaded in SRA format and in order to analyze the data in SVS, the files had to be converted to BAMs and then merged into a single VCF file.

Since many of you are accustomed to wrangling your data on a regular basis (or maybe you leave the wrangling to someone else), we thought we would share the secondary analysis steps we used when preparing the data. Our goal was to run the data through a common, "plain vanilla" pipeline, so that we were not relying on any special features during our downstream analysis. As such, we chose to use a combination of BWA and GATK; common tools that are often used in conjunction with each other. Continue reading »

CALL FOR ABSTRACTS: Dell Ultrabook Laptop and SVS Giveaway, Deadline January 31st
Call for abstracts

Are you ready to show your research to the world? Do you and a colleague want a free one-year SNP & Variation Suite license? Could you use a new laptop? Then we have a contest for you! As part of our ongoing commitment to empowering genetic researchers around the world, Golden Helix is hosting a research competition. All academic, government, and commercial organizations working with genetic data (regardless of species or location) are invited to apply. Your project should be using DNA-Seq, RNA-Seq, SNP, or CNV data. Submissions are due by January 31st. Find out more and apply »

Back to Basics: Importing/Exporting Data in Imputation Program Data Formats with SVS
by Greta Linse Peterson, Dir. of Product Management & Quality
Imputation Program Data Formats

We compared three imputation programs in a recent blog post. Data can be exported from, or imported into, SVS in the standard file formats for these and other imputation programs. The goal of this blog post will be to review the different tools available to both export and import data to the correct file formats. Depending on if you are running the imputation yourself, you may or may not need to perform the first three steps. Your data may also already be formatted correctly as input files for one of the imputation algorithms. Continue reading »
 
   Upcoming Webcast
Maximizing Public Data Sources for Sequencing and GWAS Studies
FEB
4
  Tues, Feb 4
12:00 pm EST

Rich repositories of genomic data are readily available in online public databases. But what can you expect when you download one of these datasets and what can that data be used for?

Webcast Registration



   Featured SVS Script
Export Impute2 Genotype Probabilities
Download » | Script repository »


   SNP-ITS
Golden Helix Partners with the Ontario Genomics Institute
This partnership will accelerate human health and agricultural genomics research across Ontario.
Press Release »


Advancing Agrigenomic Discoveries with Sequencing and GWAS Research
View Webcast »

Where will we see you next?
Tri-Con Short Course:
Knowing Your NGS Upstream: Alignment and Variants
San Francisco, CA  |  Sunday, Feb 9


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Recent Customer Success Highlights

Journal of Neurogenetics
Variations in Potassium Channel Genes Are Associated With Breast Pain in Women Prior to Breast Cancer Surgery
Langford, D et al.
University of California
Read the article »

PLoS ONE
ERBB2 in Cat Mammary Neoplasias Disclosed a Positive Correlation between RNA and Protein Low Expression Levels: A Model for erbB-2 Negative Human Breast Cancer
Santos, S et al.
University of Tras-os-Montes and Alto Douro, Portugal
Read the article »

Genes & Immunity
Screen of whole blood responses to flagellin identifies TLR5 variation associated with outcome in melioidosis
Chantratita, N et al.
Mahidol University, Thailand
Read the article »


 
About Golden Helix
Golden Helix has been delivering industry leading bioinformatics solutions for the advancement of life science research and translational medicine for over 15 years. Our innovative technologies and analytic services empower scientists and healthcare professionals at all levels to derive meaning from the rapidly increasing volumes of genomic data produced from microarrays and next-generation sequencing. With our solutions, hundreds of the world's top pharmaceutical, biotech, and academic research organizations are able to harness the full potential of genomics to identify the cause of disease, improve the efficacy and safety of drugs, develop genomic diagnostics, and advance the quest for personalized medicine. Golden Helix products and services have been cited in over 800 peer-reviewed publications.

 



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