Share this page!

David Eccles 🩹🩹🛡️🩹 Profile picture
Twitter logo
Feb 10 • 4 tweets • 2 min read
#SeenOnReddit Apparently SRR13441704, SRR13441705, and SRR1344170 contain hits to the SARS-CoV-2 genome.

reddit.com/r/COVID19/comm…

Reddit commenters are suggesting index hopping contamination.

doi.org/10.21203/rs.3.…
"they had sequenced the samples with Sangon Biotech (Shanghai) after extracting the DNA in December 2019 from their samples.... They deleted the three most contaminated samples from the Sequence Read Archive. They do not know why the samples were then "un-deleted."
I'll make a mental note to add "accidentally attributing SARS-CoV-2 sequences to Antarctic metagenome sequences from 2018" to my commentary on the perils of chimeric reads if I'm ever asked to present on that again.

f1000research.com/slides/8-1947 Why Does It Matter? * Low-abundance Amplicon Quantification
For people who are curious what other samples are being sequenced at the same time as their samples, I recommend fishing through the unmapped (or otherwise unexpected) reads of your own samples.

• • •

Missing some Tweet in this thread? You can try to force a refresh
　

Keep Current with David Eccles 🩹🩹🛡️🩹

David Eccles 🩹🩹🛡️🩹 Profile picture

Stay in touch and get notified when new unrolls are available from this author!

Read all threads

This Thread may be Removed Anytime!

PDF

Twitter may remove this content at anytime! Save it as PDF for later use!

Try unrolling a thread yourself!

how to unroll video
  1. Follow @ThreadReaderApp to mention us!

  2. From a Twitter thread mention us with a keyword "unroll"
@threadreaderapp unroll

Practice here first or read more on our help page!

More from @gringene_bio

David Eccles 🩹🩹🛡️🩹 Profile picture
Nov 4, 2021
Marsden Fund: is it worth it?

The Marsden Fund is a competitive fund in which the "top" researchers are given money to do proposed research.

This year, $82,345k was awarded to 120 projects. That's a mean of ~$230k per project.

#StopCompetitiveFunding
When considering 100% institute overheads, that ~$230k over 3 years ends up as enough for 1.5 researchers at Massey's Step 1 lecturer salary ($74k).

Unfortunately those 120 projects had 394 named investigators, or around 3.3 investigators per project.

massey.ac.nz/massey/about-m…
Research costs? What research costs?

The Royal Society has this year provided information on Marsden applications:

royalsociety.org.nz/what-we-do/fun…

Did I mention that Marsden is a *competitive* fund? That pretty much means researchers need to do pre-research to have a chance...
Read 11 tweets
David Eccles 🩹🩹🛡️🩹 Profile picture
Nov 3, 2021
I've been looking at all these plots about vaccine effectiveness and hospitalisation, and thinking they're missing the exposure side of things... so I made another plot.

This plot shows how the vaccine reduces both hospitalisations *and* disease.

gitlab.com/gringer/covid-… otearoa Case Vaccine Demogr...
I've assumed here that the number of exposed unvaccinated people is the same as the number of unvaccinated people with COVID. I could bump that exposure number up a bit, but it wouldn't change the overall visualisation because the proportions of vaccinated people wouldn't change.
There's another niggle in that vaccination & cases are a dynamic event. MOH doesn't have vaccination status in their case demographic CSV file, so I use 2 wks ago as a fudge.

That shouldn't be too much of a problem anyway, because recent numbers dominate for exponential growth.
Read 4 tweets
David Eccles 🩹🩹🛡️🩹 Profile picture
Jul 24, 2018
The National Ethics Advisory Committee's National Ethics Standards for Health and Disability Research are now open to the public for feedback:

consult.health.govt.nz/neac/national-…
I'll comment on the initial principles of this now in regards to the recommendations I've previously made public:

gringer.gitlab.io/presentation-n…

In short, they're great. My main comments are around needing more emphasis on participant control - making that implicit principle explicit.
"Researchers are expected to learn as well as gather data in research, to collaborate and to give back to the community (eg, through koha and sharing ideas)." [S 5.7] - a good principle to have; I think a minimal sharing protocol needs to be specified in ethics applications.
Read 24 tweets

Did Thread Reader help you today?

Support us! We are indie developers!

This site is made by just two indie developers on a laptop doing marketing, support and development! Read more about the story.

Become a Premium Member ($3/month or $30/year) and get exclusive features!

Become Premium

Don't want to be a Premium member but still want to support us?

Make a small donation by buying us coffee ($5) or help with server cost ($10)

Donate via Paypal

Or Donate anonymously using crypto!

Ethereum

0xfe58350B80634f60Fa6Dc149a72b4DFbc17D341E copy

Bitcoin

3ATGMxNzCUFzxpMCHL5sWSt4DVtS8UqXpi copy

Thank you for your support!

Like this author's thread?

Get emails when @gringene_bio has new unrolls!

Check out other threads from @gringene_bio!

Read all threads by @gringene_bio

:(