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SNP-workshop-minutes.docx

snp-survey-responses.pptx


Contact: Scott Cornman, rcornman@usgs.gov

Minutes:

1) People expressed interest in viewing webinars, not necessarily enthusiastic about giving one. Hopefully people are willing to talk about their projects and technical issues under coercion, so that we could produce a collection of talks a la the eDNA webinars.

2) Damian suggested a co-occurring workshop with GEDWG technical exchange (Tampa area, mid January?). General agreement that this would be a good idea, although that might present a conflict for me personally, I’d probably have to be virtual.

3) Aaron highlighted the art/practice of SNP filtering/ascertainment as a topic, echoed by Sarah.

4) David was particularly interested in analysis of the snp data sets once produced. There is a collective body of knowledge for that, based on work people have done. I’m no expert on applications. Leetown and Alaska would probably have a lot of knowledge about population assignment/stocks; FORT has been doing outlier/correlative work on local adaptation, which Alaska is getting into too.

5) I am available for site visits for custom consultation. My preference is to minimize travel, but if there is a group of people at one place, obviously it makes sense for me to go there.

6) Suggestion: identify web tutorials, review papers, R vignettes, etc. that you think are good, could form the basis of a curriculum.

7) There are a lot of gems hidden in the skulls of lab practitioners and customer service representatives that represent hard won technical knowledge. Not sure how to efficiently share these. Probably it pays to do a first library prep in an experienced lab whenever possible.

Basic skills (which Scott can teach):

a)  Generate vcf from raw fastq and a reference

b)  Filter and plot SNP variables/biases and choose filtering appropriate for my project

c)   Convert a vcf to input for popgen software and run basic analyses

       i)    F statistics, genetic distance, PCA, dendrograms, clustering

Advanced applications (team taught):

d)    Advanced clustering/assignment/Ne analysis

e)    Baypass/BayEnv/BayScan.

f)    Genome-wide association studies          

g)   Microsatellite genotyping via high-throughput sequencing                                        

Conclusions:

i)  A webinar series seems too much for this base of participants.

ii)  Suggest one webinar on high-throughput genotyping methods, focused on the technical problem and solution, not the biological question. Led by ASC and LSC.

iii)  Suggest a second webinar or virtual workshop that would cover the basics of SNP calling and variant filtering.

iv)  Leave open the possibility of a hackathon occurring before or after conferences

    (1) Tutorials 

    (2)  Writing session for proposals or completed projects

    (3)  Discussions: how could we adapt what so-and-so did in their talk to our questions?



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