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
  • Andrew
  • 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
    • 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


  • 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?

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 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!