20th Discussion-6 Feb 2018
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- 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
- Russell Hamilton - University of Cambridge
Please add yourself...
- 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"
- command line, common bioinfo tools
- RNA-seq / ChIP-seq / application specific
- someone suggested github / docker
- Simon said they do
- 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
- 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?
- 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?
- 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 article about novaseq
- Also 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!