Difference between revisions of "20th Discussion-6 Feb 2018"
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== Attendees == | == 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 == | == Training == | ||
| Line 6: | Line 19: | ||
* Do you have any requirements to entry? | * Do you have any requirements to entry? | ||
* What are your favorite platforms for teaching or teaching tips? | * 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 == | == Nanopore == | ||
| Line 11: | Line 59: | ||
* Which tools have you found useful thus far for analysis? | * Which tools have you found useful thus far for analysis? | ||
* Any particular quality control approaches you are using? | * 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? == | == Other New Protocols or Approaches? == | ||
* Anything new happening at your institution that you would like to discuss? | * 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! | ||
Latest revision as of 13:51, 8 February 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 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!
