In this webcast, Ashley Hintz, Field Application Scientist, will address some common topics fielded by our support team. Topics will include the following: Custom Genomes: Currently SVS has a large data repository of annotation data sources from a wide variety of human, animal and plant genome assemblies. Additionally adding a custom genome to SVS has become quick and easy using our new Annotation Convert Source Wizard. We will show you how to create an allele reference sequence track using a FASTA assembly file and gene annotation track using a GTF annotation file. Sample Collated Spreadsheet: Use the Build Sample Collated Spreadsheet function to create a per marker summary of your available sample information. For example if you have imported genotypes, read depths and genotype qualities for all your samples you can create a summary of those values for each sample at each marker location. Activating/Inactivating Data: SVS has a variety of ways to activate or inactivate data for further analysis. We have tools available that can activate your data based on a list of marker names or based on genomic position as well as tools that can inactivate duplicate values.

1. Tips and Tricks for
Genomic Analysis
in SVS
August 6, 2014
Ashley Hintz
Field Application Scientist

2. Questions during
the presentation
Use the Questions pane in
your GoToWebinar window

3. Agenda
Tips for DNAseq
Questions!
2
3
4
Data Management Tricks
Build Custom Genome
1

4. Core
Features
Packages
Core Features
 Powerful Data Management
 Rich Visualizations
 Robust Statistics
 Flexible
 Easy-to-use
Applications
 Genotype Analysis
 DNA sequence analysis
 CNV Analysis
 RNA-seq differential
expression
 Family Based Association
SNP & Variation Suite (SVS)

5. GenomeBrowse
 Free sequencing visualization tool
 Launched in 2011
 Makes the process of exploring
DNA-seq and RNA-seq pile-up and
coverage data intuitive and powerful
 Stream public annotations via the
cloud
 Use it to validate variant calls, trio
exploration, de Novo discovery, and
more

6. Agenda
Tips for DNASeq
Questions!
2
3
4
Data Management Tricks
Build Custom Genome
1

7. Tips for DNASeq
• Ability to create a collated and
filtered spreadsheet from
multiple inputs
• Outputs data from where all
spreadhseets overlap
• Sample use case – de Novo
Variants
• Script: Join or Merge Several
Spreadsheets
www.pseudomonas-syringae.org

8. Agenda
Tips for DNASeq
Questions!
2
3
4
Build Custom Genome
1
Data Management Tricks

9. Data Management Tricks
• Activate by Gene List
• Activate by category in data
columns
• Markers in LD block subset
in Genome Browse
• Script: Activate/Inactivate
based on Genomic Position
• Script: Inactivate Duplicate
Column Headers

10. [Demonstration]

11. Agenda
Tips for DNAseq
Questions!
2
3
4
Data Management Tricks
1
Build Custom Genome

12. Build Custom genome
 Anopheles gambiae (Mosquito)
 Arabidopsis thaliana (Thale Cress)
 Bos taurus (Cow)
 Brassica rapa (Napa Cabbage)
 Caenorhabditis elegans (Round Worm)
 Canis familiaris (Dog)
 Capra hircus (Goat)
 Capsicum annuum (Hot Pepper)
 Carica papaya (Papaya)
 Citrullus lanatus (Watermelon)
 Cricetulus griseus (Chinese Hamster Ovary- CHO)
 Danio rerio (Zebrafish)
 Drosophila melanogaster (Fruit Fly)
 Equus caballus (Horse)
 Eucalyptus grandis (Eucalyptus)
 Felis catus (Cat)
 Gallus gallus (Chicken)
 Glycine max (Soybean)
 Gossypium raimondii (Cotton D)
 Heterocephalus glaber (Naked Mole-Rat)
 Leishmania infantum JPCM5 (Leishmania parasite)
 Macaca mulatta (Rhesus Monkey)
 Mus musculus (Mouse)
 Onchorhynchus mykiss (Rainbow Trout)
 Oryza sativa (Japanese Rice)
 Ovis aries (Sheep)
 Prunus persica (Peach)
 Rattus norvegicus (Norway Rat)
 Saccharomyces pombe (Baker’s Yeast)
 Sorghum bicolor (Sorghum)
 Sus scrofa (Pig)
 Zea mays (Maize)

13. Build Custom Genome
• Anolis carolinenesis – Carolina
Anole Lizard
• Downloaded from Ensembl
• Reference Genome
• Separate FASTA file for each
chromosome
• Gene Track
• Single GTF file
• Originally published in Nature by
Alföldi et al. (2011)
• 6 macro-chromosomes
Photo courtesy R. Colin Blenis
• Draft assembly 1.78GB
• 17,472 protein-coding genes
• 2,924 RNA genes www.pseudomonas-syringae.org
Photo courtesy Robert Michniewicz

14. Build Custom Genome

15. Build Custom Genome

16. Build Custom Genome

17. Build Custom Genome

18. Build Custom Genome

19. Build Custom Genome

20. Build Custom Genome

21. Build Custom Genome

22. [Demonstration]

23. Questions or
more info:
 Email
info@goldenhelix.com
 Request an evaluation of
the software at
www.goldenhelix.com