owlmonkey

8 ms·

1.
by owlmonkey 7y ago
One study says ~38 individual base mutations per generation, but that increases by about 2 bases per year of the father's age, which is still not much given 6 billion base pairs in humans. ( https://www.ncbi.nlm.nih.gov/
2.
by owlmonkey 10y ago
If one of these jackknifes enroute is that called a 'snowcrash'?
3.
by owlmonkey 10y ago
It's politics. You can't survive here politically proposing as-of-right building permits and across the board upzoning. But you can move the needle in the right direction.
4.
by owlmonkey 10y ago
Building is the one variable of the three he cites that is reasonable to encourage IMO. But the pre-existing population here has demonstrated a clear disdain for building. So who is really to blame then for the inflation and displacement an
5.
by owlmonkey 10y ago
TILT sounds like an interesting idea. In San Francisco I suspect our best bet is through California State laws offering density bonuses or provide as-of-right building in some form, that overrides local planning constraints. For example, AB
6.
by owlmonkey 11y ago
The implication is that people are illegally listing multiple properties that they own or rent, but this analysis doesn't rule out the cases where someone hires a professional property manager to list their place on AirBnB while they&#
7.
by owlmonkey 11y ago
I don't follow your train of thought on in-laws. Because they're small, they're unlikely to serve for 'hosted' rentals and more likely to be only short term rentable up to 90 days. e.g. when the existing renter in t
8.
by owlmonkey 11y ago
Not any more, and especially not compared to the HiSeq 2000 used for that paper. PacBio's raw sequencing cost is now about on par with where the HiSeq was when it first launched. And because of the error profile you don't need as
9.
by owlmonkey 11y ago
If they were really interested in discovering unknown genes, they should have used PacBio to sequence the whole genome instead of just 83% of it via Illumina. That assembly quality ("a contig N50-length of 5.4 kb and a scaffold N50-len
10.
by owlmonkey 12y ago
Better to have people looking in the wrong place, in a way that they will look indefinitely
11.
by owlmonkey 12y ago
Totally agree with you on the computation costs. In some slides in February ONT hinted at why they had to go to a full wet sample prep and it related to input DNA amounts I believe. Their new sample prep they said allowed them to reduce the
12.
by owlmonkey 12y ago
Ya the MinIon is more of a DNA sensor than a sequencer in its current incarnation, but awesome for portability. Super expensive per base though. If they can't improve the cost significantly along with the accuracy it will never be a co
13.
by owlmonkey 12y ago
Totally agree. It is at best a semi-portable sensor (with wet prep) not a sequencer. Cost would be another big obstacle for using MinIon on human data. At about 100 megabases and $1000 per cell that's three orders of magnitude more exp
14.
by owlmonkey 12y ago
One doesn't need CCS anymore, though it is still an option for shorter insert lengths. The errors are more random than other platforms, so they resolve easily with consensus. You just need 20x coverage or more, depending upon the appli
15.
by owlmonkey 12y ago
PacBio is ultimately more accurate than Illumina given consensus. Illumina has some systemic bias so the ultimate accuracy tops out around Q40-Q50 (same errors just repeat themselves) and PacBio will get you closer to Q60-Q70 because the ra
16.
by owlmonkey 12y ago
Another researcher was sequencing Brook before she died, and I believe using the PacBio sequencer to get the full sequence (instead of an incomplete "whole" sequence using Illumina sequencers.) Hopefully something useful will emer
17.
by owlmonkey 12y ago
Haven't tested on 3.2.x yet but the GC was never the issue for our stress tests. Bugs in the socket layers were killing us. Better under 2.10.9 but still not completely resolved.
18.
by owlmonkey 12y ago
We have a product that has a C# web app deployed via mono on a linux box commercially shipping for four years. What I found was that with mono 2.10.6 it was fine as long as it was not loaded heavily, but under stress it would have stability
19.
by owlmonkey 14y ago
Some interesting structural differences are not captured by 23andMe nor even with technology like Ion Torrent, for example repeat sequences related to ALS, Huntington's, etc. To get the full picture ultimately you'll need a full sequence wi
20.
by owlmonkey 14y ago
I agree PacBio doesn't have the high-throughput of Illumina or similar amplification approaches yet, but from last month's AGBT conference papers it's clear that it's now more accurate than other systems with typical coverage (no bias, cove
21.
by owlmonkey 14y ago
PacBio has average read length now of about 5000 bp whereas 454 is still only about 1000 bp.