Date
Participants
and more….
Discussion topics
Time | Item | Presenter | Notes |
|---|---|---|---|
· New public Confluence site allowing easier access for everyone https://gobiiproject.atlassian.net/wiki/x/A4AKB | Liz | ||
· Slack channel now created |
| ||
Review meeting agenda CIP May https://gobiiproject.atlassian.net/wiki/x/IgEIB Tour of genebank facilities Friday? | Marcello | Carpentries Lindsay - Dorcus send out an email for interest. Need R and R studio set up - Lindsay will |
send out specifications Umesh and Marcello and Trushar can help, Liz talk earlier - Friday and then Lindsay Get a number count for the genebank tour closer to the time - Friday afternoon is good Need for vcf filtering tools - Lindsay and Marcelo can cover Lindsay recommends an R package - VariantAnnotation (Bioconductor) Read depth - how this affects calling dosage? sweet potato need 100X - Jeff’s talk will cover this and Lindsay will too Small numbers of markers - eg amplicon technologies , KASP dosage for potato - Petra says can do now - Eng present on technologies for polyploids. Luis has genotyped with the fluidigm system with Cassava - converted Illumina markers. 50/50 dosage | |||
Review crop specialist needs – crop contacts https://gobiiproject.atlassian.net/wiki/x/KQEIB | Dorcus | ||
Local arrangements Recordings | Dorcus | Would be good to get recordings and can post them on the EiB website | |
Visa requirements for Americans? | Jeff | None - Dorcus will check - no, none needed | |
Dataset sharing site | Liz | Github? Marcelo - Mapping section have a vcf F1 population with 2 hexaploid parents Can also be used for haplotyping - Umesh will present haplotyping in populations Dorcus have any tetraploid F1 datasets? No but have a GWAS panel Marcelo has public datasets for F1 tetraploids Linsday may use a different dataset for GWAS Key datasets Mapping - F1 triploids (Trushar), tetraploid (SolCAP) and hexaploid (Marcelo) GWAS - diversity population - tetraploid (Umesh has) and hexaploid (Dorcus has raw data) Data types: vcf, Illumina chips (banana) |
Challenge - don’t know the ploidy level (single dose markers?)
Action items
Action items
- Dorcus Gemenet to get technical support to do video recordings on Day 1 and 2
- Elizabeth Jones to send Dorcus info on ppt Friday
- Lindsay Clark to send Dorcus info on what is required (laptop set up, minimum skills) for attendees for Carpentries session Friday
- Dorcus Gemenet to send out Friday open-session details to relevant CIP teams and see who is interested. For approx 25 people?
- Marcelo Mollinari to send out Github link so people can post datasets there
- Marcelo Mollinari to discuss with team whether we need extra time for variant calling pipelines and vcf filtering tools - lots of interest from the group. If we do this Friday we may not have time for Carpentries session