aroch

6 ms·

1.
by aroch 1y ago
> However–and here’s the rub–some 25 years after the human genome was sequenced, and despite huge efforts to link genes and disease, there are almost no SNPs that tell you anything consequential about your health. If you have a genetic d
2.
by aroch 1y ago
I’m a fan of Saramonic’s MV2000 ( https://saramonicusa.com/sr-mv2000-large-diaphragm-usb-studi... ) is an affordable, good quality cardiod mic. Frequently available for $50 and supports live headphone pass through if that’s y
3.
by aroch 2y ago
I have ‘ccat’ aliases to the original cat binary
4.
by aroch 4y ago
Nebula most likely ship your samples to China for processing and sequencing because it's so much cheaper. While that might not be a deal breaker for some, I would personally prefer my sample not be shipped elsewhere.
5.
by aroch 4y ago
Eh, your results look perfectly fine, especially for a budget sequencing run. Keep in mind there are a lot of repetitive DNA sequences that don't map well (search "mappability track" for more info). Depending on the reference
6.
by aroch 4y ago
No one should be BLASTing individual reads... And pretty much no one is going to be assembling with OLC, even for ONT data. On the products page it says they provide FASTQs, aligned BAM and VCF. Which is exactly what one would expect. They
7.
by aroch 4y ago
Not for home gamers, no. ONT is fairly low throughput and the prep is surprisingly difficult to do well without experience. You would need to run tens of flow cells to get enough sequencing data.
8.
by aroch 4y ago
I have no skin in this particular game (Though I work in the sequencing industry), but... I don't think anyone is fooled/trying to trick anyone when they say "whole genome sequencing" or that they sequence 100% of the g
9.
by aroch 5y ago
Lifetime license does not mean lifetime support. I get that that might be annoying, but why or how could they warranty third party software, that they don't control or version themselves, indefinitely?
10.
by aroch 5y ago
Yes, but if your child is school age -- schools which are now increasingly going to in person instruction -- and you are immunocompromised, what are you going to do? Same question if you live in a multi-generational household, but now ther
11.
by aroch 5y ago
Not necessarily, you could have an immuno-compromised parent/grandparent
12.
by aroch 5y ago
The point of vaccinating kids is: 1. They still get sick, even if asymptomatic, and can bring it home to the house where older people live 2. I don't know if there are published case report / data yet, but anecdotally the new st
13.
by aroch 6y ago
The answer to "Why are they investigating?" is simple and, in fact, driven in part by the pharmaceutical industry itself. First: The rate of thrombosis in AZ recipients is the less than it is in the general population -- Gen pop
14.
by aroch 6y ago
If you have a new model, hold the ionizer button for 5 seconds and the indicator light will turn off.
15.
by aroch 6y ago
Strongly suggest using Let's Plot from JetBrains instead. It's much closer to ggplot2 in api and results. https://github.com/JetBrains/lets-plot
16.
by aroch 6y ago
The Telomere-to-Telomere consortium has made fantastic progress on this in the last year or two: https://genomeinformatics.github.io/CHM13v1/ Thanks to them we now have a nearly completed genome, only missing the decon
17.
by aroch 6y ago
Sample prep, particularly if you want truly long reads, is 100% the hardest part. Funnily, there are people out there who want to teach army/marine grunts on the front line to run minIONs. Most of the work is on making the sample prep
18.
by aroch 6y ago
This isn’t the case anymore. Pathogen surveillance labs use Nanopore for single-base resolution variant calls to determine antibiotic susceptibility and to “fingerprint” against known and previously sequences isolates.
19.
by aroch 6y ago
I think you're stuck in the biotech == people mindset. On the bacterial side, it is fantastic for quickly sequcinging and closing genomes. Personally, I think the killer use case is field portable and real time sequencing of pathogens
20.
by aroch 6y ago
Over the last few years there have been several (4-5) instances of British subs nearly striking surface ships in their home waters. Also running aground right outside their home port in 2010. Not exactly reassuring. The US Navy is much bigg
21.
by aroch 6y ago
Calling the British navy a battle ready fleet would be rather a positive attitude. Their submarine and surface ship captains don't know how to navigate, running aground and into other boats. And their aircraft carriers don't even
22.
by aroch 6y ago
Ah, I think so!
23.
by aroch 6y ago
Oh Haxies, I remember writing run-time patches (aka, cracks) to bypass licensing/registration for several pieces of software. There was a common framework, whose name no eludes me, that could be almost universally patched giving acces
24.
by aroch 6y ago
Lead dev here. While you're not wrong that we might be under-estimating risk, I'll note that we do take into consideration seroprevalence in our calculations (so called, ascertainment bias). We provide estimates for two cases; 5x
25.
by aroch 6y ago
Lead dev here... Huh, didn't think I'd ever see my work show up on HN. Sadly getting an .edu institution to fork over the money for better scaling is hard... Even when it gets them unlimited free press.
26.
by aroch 6y ago
The easiest is to send e-coupons to frequent shoppers?
27.
by aroch 6y ago
You see them a lot in biological network / pathway / association studies. I personally hate them, because they're hard to read and comprehend. Many times a heatmap conveys the exact same data in a more digestible way. Alas
28.
by aroch 6y ago
Oh, hmm, that's very interesting and not something I would have thought about! :)
29.
by aroch 6y ago
That was our feeling about the two products as well, the limitations w/ TileDB-vcf though sort of forced our hands. I was (and still am) of the opinion TileDB would be a good variant store since it does do so many of the things we wan
30.
by aroch 6y ago
Hail.is is what we landed on. There are some things we don't like with it too but weren't deal breakers

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