View source for 20th Discussion-6 Feb 2018

== Attendees ==
* Brent Richter - Partners
* Alberto Riva - University of Florida
* Alastair Kerr - University of Edinburgh
* Madelaine Gogol - Stowers Institute
* Matt Eldridge - Cambridge
* Simon Andrews - Babraham Institute
* Cory Brauer - UNC Charlotte
* George Bell - Whitehead Institute
* Mark Berres from UW Madison
* Yury Bukhman - Morgridge Institute for Research, Madison WI
* Andrew
* Russell Hamilton - University of Cambridge
Please add yourself...

== Training ==
* How much does your core do, and how do you schedule it? 
* What do you teach?
* Do you have any requirements to entry?
* What are your favorite platforms for teaching or teaching tips?

How much training do you do?
* 2-3 full days modeled on software carpentry, done a few times, command line, RNA-seq
* Simon Andrews, Babraham Institute
** huge amount of training, 50 courses a year, a day each
** one of their core functions
** internal / external / commercial venture
** 5 regular teachers
* Matt Eldridge, Cambridge
** Also a large amount of training
** Part of a larger university program
** demand is massive, long waiting list
** perhaps have noticed routine analysis going down in volume
*** maybe that's fine, let routine stuff go and focus on harder analyses
* How much? free?
** 50 pounds a day for postdocs, Phd students free
** 178 pounds a day with a "day rate"

Curriculum?
* command line, common bioinfo tools
* RNA-seq / ChIP-seq / application specific
* someone suggested github / docker
* Simon said they do
** statistics
** core skills - unix, perl/python, R
** RNA-seq / chIP-seq / methyl-seq
** "creating figures"
** gene set enrichment analysis
* Goblet was mentioned
** but direct reuse is harder than it seems
* Environments are tricky
** how do you ensure the same environment for everyone?
** amazon - but then dependent on network
** some people use docker - last part of course is getting things running on *your* laptop
** Use a script to check that everything is installed and ready to go

== Nanopore ==
* How is your core supporting Nanopore sequencing?
* Which tools have you found useful thus far for analysis?
* Any particular quality control approaches you are using?

Nanopore
* Who is doing it and what are your experiences?
* Now they have a direct RNA sequencing kit
* minoTour - realtime nanopore monitoring
* Mark, UW Madison - quality of flowcells drops considerally, they run 32-36 hours
* Nanopore is operator / library sensitive
* air bubbles in flowcell can happen
* EDTA will kill it
* Minknow is the software from oxford nanopore, mac/linux/windows, downstream albacore
* smaller flowcells are coming - running a smidgeon on a minion
* minion_qc on github useful QC plots, minimap2 for alignment
* epitome from ONT
* WIMP - what's in my pot
* how about base modifications?
** nanopolish can report methylated bases, but some question about accuracy. Paper in nature methods
** Simon mentioned trying to use it to assemble immunoglobulin, found nanopolish was over collapsing their reads

== Other New Protocols or Approaches? ==
* Anything new happening at your institution that you would like to discuss?

Upcoming technologies?
* FPGA / GPU
** GPU will win out, maybe
** Intel is pushing FPGA
** Brent says mostly GPU for their machine learning / AI applications

* Phil Ewels has a github site with tools to examine Novaseq
* Simon mentioned qcfail.com [https://sequencing.qcfail.com/articles/the-latest-illumina-sequencers-muddle-samples/ article] about novaseq
* Also [http://10xqc.com/ 10xqc.com] for uploading/sharing cellranger reports, nice!

ISMB Workshop, 2018 chicago
* Hiring / interviewing strategies
* Containers / clouds
* lightning talks, unconferencing small group discussions
* We'll be looking for speakers
* Let us know if you want to help organize it!