Noah Reid @NM_Reid Twitter profile

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Noah Reid

@NM_Reid

19 days

uhh, anaconda just sent a message to our HPC admins that we're in violation their ToS and we now need to pay for a license or remove all their software from our system?

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Noah Reid

@NM_Reid

6 years

I wonder if middle authorship, when you really care about the paper, is like being a grandparent: you get to do a bunch of the fun parts, and first and last author parents have to clean up all the shit.

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Noah Reid

@NM_Reid

3 years

I feel like bioinformatics and bike maintenance have a lot in common: a multitude of standards, impenetrable documentation, weird multifactorial dependencies, everything just generally being dirty and fiddly, but from the outside it all seems like it should be so simple.

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Noah Reid

@NM_Reid

3 years

somehow I think the people hyping containerized workflows as a way to enable reproducibility did not anticipate the side effect "now everyone can just run pipelines they don't understand full of software they don't understand to get results they don't understand."

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Noah Reid

@NM_Reid

4 years

my hobby: giving collaborators sets of bam files that have been aligned to slightly different reference genomes without telling them.

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Noah Reid

@NM_Reid

19 days

I cannot imagine anaconda/miniconda could have become so ensconced in academic software development if people had not believed it was/would be free, at least for academic use.

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Noah Reid

@NM_Reid

3 years

8yo tells 6yo that Dimetrodon is not a dinosaur. 6yo pitches a fit, screams that it is. Daddy tries to teach them both tree thinking, inadvertently solving the dispute by boring them so much they just want to get back to playing.

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Noah Reid

@NM_Reid

19 days

it seems totally bonkers to release an apparently free package installer that provides users and admins no warning that a paid license is required, wait YEARS, and then come knocking and demanding to be paid.

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Noah Reid

@NM_Reid

3 years

As part of a two-body problem that did not get resolved the way we wanted, I do not think this article is helpful or remotely reflects the barriers we faced.

One scientist couple’s five suggestions to solve the ‘two body problem’

Nature - Sarah A. Gagliano Taliun and her husband made a Plan A, but were prepared to re-evaluate their priorities to find jobs where they could live together.

www.nature.com

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Noah Reid

@NM_Reid

5 years

I'm happy to announce this paper on adaptive introgression leading to pollution tolerance in killifish.

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Noah Reid

@NM_Reid

5 years

It seems like there should be a german word for the feeling you get when you've searched google scholar on a topic 100 times and then somebody tells you about a paper with a million citations and all your key words in the title and you somehow missed it.

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Noah Reid

@NM_Reid

3 months

I genuinely can't believe that someone had to write this paper in 2024. Any application of SNP data that depends on accurately identifying heterozygous genotypes is going to be STRONGLY INFLUENCED by depth of coverage.

Dr. Jon Puritz (@jonpuritz.bsky.social)

@JonPuritz

3 months

A must read for anyone studying population genomics. Low-coverage sequencing and Wahlund effect severely bias estimates of inbreeding, heterozygosity and effective population size in North American wolves

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Noah Reid

@NM_Reid

5 years

1980s: here: admire my fine table of Fst values. 1990s: look at this gene tree! so much better than stupid old Fst! 2000s: that tree is lying. to. you. fit this model instead! 2010s: ok I have a genome and your stupid model won't even run I'm just going to calculate Fst. 2019:

Kelley Harris

@Kelley__Harris

5 years

Congratulations to @jeromekelleher , @gil_mcvean , @leo_speidel , and @simon_r_myers on publishing their fabulous new methods for inferring genealogical trees from whole genomes! Here's my take on why these papers make it a great day for population genetics:

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Noah Reid

@NM_Reid

3 years

I'm curious about examples of strong genetic differentiation in eukaryotes on very small scales. I'm helping out on a study of a desert plant species where populations 250m apart separate out cleanly in a PCA. it kind of blows my mind.

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Noah Reid

@NM_Reid

4 years

So, anyone want to share their favorite R code for making structure/admixture plots?

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Noah Reid

@NM_Reid

2 years

is this a hot-take? when you need a phylogeny, sometimes a neighbor-joining tree on uncorrected distances is good enough to make a point and a more intensive analysis is pointless extra effort.

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Noah Reid

@NM_Reid

19 days

I don't know what "The Register" is, but

Anaconda puts the squeeze on data scientists

Academic, non-profit organizations told to start paying up – or else

www.theregister.com

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Noah Reid

@NM_Reid

4 years

Unpopular opinion: virtually all words and phrases in this thread are fine and banning them would do literally nothing to improve the readability of scientific literature.

Jeff Craig

@DrChromo

4 years

What words would you have banned in science? I'll start: "elucidated"

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Noah Reid

@NM_Reid

5 years

When you finish a PhD in phylogenetics they try to take you to a special room to tell you something but there are just so many rooms they can't guarantee they've taken you to the right one, so they keep trying new rooms and eventually they just give up and tell you to postdoc.

Erol Akcay

@akcayerol

5 years

When you finish a PhD in theoretical ecology, they take you to a small room and tell you all models are correct and most are useless. I’m posting this at great metaphysical risk to myself and my family.

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Noah Reid

@NM_Reid

6 years

if machine learning can't tell me who wrote the anonymous trump op-ed then I don't want to hear another damn word about it solving all of evolutionary biology.

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Noah Reid

@NM_Reid

4 years

I can't believe chromosome-scale genome assembly papers are the new "10 microsatellite loci isolated from species X".

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Noah Reid

@NM_Reid

5 years

Wow, what a glowing review of @DocEdge85 's "Statistical Thinking From Scratch". I'm going to check it out!

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Noah Reid

@NM_Reid

7 years

In which R. Alexander Pyron argues that the sixth mass extinction doesn't matter because in 50m years, there will be a fantastic diversity of roaches.

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Noah Reid

@NM_Reid

2 years

I'm interested in recent books on genome biology/evolution along the lines of Lynch's Origins of Genome Architecture, which is now 15 years old. Any suggestions?

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Noah Reid

@NM_Reid

8 years

Hot off the presses! Evolution of pollution tolerance in killifish. By me. In @sciencemagazine

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Noah Reid

@NM_Reid

5 years

I would love to know how many gene-phenotype or gene-environment associations in conservation genetics and molecular ecology stand up to increased sampling, replication, or external validation of some kind.

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Noah Reid

@NM_Reid

2 years

This R package wants me to run a function that will install software on my system. It has code that literally asks for my password and then runs 'system("sudo -kS sh -c 'make install; ldconfig'", input = password)' An R function secretly running sudo seems so, so sketchy

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Noah Reid

@NM_Reid

3 years

lest you think I'm subtweeting, it's me. I'm everyone in this scenario. singularity go brrrrrrrr.

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Noah Reid

@NM_Reid

4 years

@mike_c_mahoney ... is destructive. I wish I knew how I came around to it, I think we all know that simple facts rarely convince people with strong feelings, but I'll never have an outdoor cat again.

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Noah Reid

@NM_Reid

3 years

I have long gotten misdirected e-mail intended for a certain beloved Canadian actor from Schitt's Creek. Today a guy asked me to make a video wishing his girlfriend, who is a huge fan, a happy birthday. Thinking about doing it.

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Noah Reid

@NM_Reid

5 years

fascinated by the gay genes study? this is a great time to read (or reread) this blog post by @Graham_Coop on the complexities of understanding the genetics of human traits. it's largely focused on btwn population diffs, but still totally relevant.

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Noah Reid

@NM_Reid

19 days

Anyone else experiencing this?

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Noah Reid

@NM_Reid

5 years

throwing my 2c in on the retraction scandal: 1) twitter *can* be horrible, but the response to this I am seeing is so generally mature and supportive of the folks who are hurt by it, that I am encouraged.

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Noah Reid

@NM_Reid

4 years

I don't know who needs to hear this, but good editing is so much more than ruthlessly scratching out "elucidate" and "in order to". In fact, I think attending to those is a complete distraction from an editor's real task of helping to organize and clarify ideas.

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Noah Reid

@NM_Reid

5 years

Is it too early to plug your stuff for #Evol2019 ? I'm giving a poster on Sunday on a cool project I've been working on: sex chromosome evolution and sex determination in two species of killifish.

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Noah Reid

@NM_Reid

6 years

I'm glad I've restricted most of my twitter follows to science. I keep getting sorely tempted to come here and rage about politics, which would not help anybody, but every time I do I get distracted by a cool paper.

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Noah Reid

@NM_Reid

6 years

It seems like there are direct estimates of mutation rates being published for many organisms, often buried in larger manuscripts. Anybody want to start putting together a google sheet to track them? Is this a silly idea?

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Noah Reid

@NM_Reid

6 years

A publicly editable google sheet initialized with my two current favorite mutation rates. I'm not sure which fields would be most useful, or which methodological details are most pertinent. I'm open to suggestions about better ways to do this.

Mutation rate estimates

docs.google.com

Noah Reid

@NM_Reid

6 years

It seems like there are direct estimates of mutation rates being published for many organisms, often buried in larger manuscripts. Anybody want to start putting together a google sheet to track them? Is this a silly idea?

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Noah Reid

@NM_Reid

6 years

@ColinJCarlson A poignant argument for methods-at-the-end, that the doomed flower of your love might bloom a moment longer.

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Noah Reid

@NM_Reid

18 days

@alonsosilva This statement seems to be in direct conflict with what we're experiencing right now.

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Noah Reid

@NM_Reid

3 years

@FedExHelp @DanielBolnick This is some black comedy gold right here.

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Noah Reid

@NM_Reid

5 years

properly simulated data will be MUCH harder to detect. and every year, mountains of graduate students in a very competitive environment are developing exactly the necessary skills. I don't know what to say except that this really disturbs me.

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Noah Reid

@NM_Reid

4 years

more digging into other people's R code... these spanish coders are using data frames named "datos" and "datitos". gonna have to steal that convention.

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Noah Reid

@NM_Reid

6 years

Well now I want to know the minimum number of individuals in the US who have to use a genetic ancestry site before no criminal who leaves DNA behind can escape detection. I'm sure that's a blog post @Graham_Coop probably doesn't want to write .

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Noah Reid

@NM_Reid

5 years

unpopular opinion(?): arbitrary stylistic choices that do not interfere with understanding should not be mocked or required to be altered by editors.

John P. Vanek, PhD

@wild_ecology

5 years

I've been caught! Decision letter from an AE: "I also ask that you purge "utilized" which is simply an "impressive" way to say use. " @StephenBHeard

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Noah Reid

@NM_Reid

19 days

@FrankBoerman I am not an expert in package management, but we don't just use conda for python packages, and frequently our users are simply following suggestions provided by software developers that they can either spend days in dependency hell or use conda.

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Noah Reid

@NM_Reid

5 years

@Graham_Coop I couldn't help but get carried away with imagining your mitochondrial and nuclear genomes discussing your degeneracy...

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Noah Reid

@NM_Reid

6 months

I resolved a little RADseq mystery... we have this dataset where there is bimodal coverage of rad sites. there is a wide, high coverage mode at ~ 100x, and a narrow low mode at ~7x (marginal Y-axis histogram).

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Noah Reid

@NM_Reid

5 years

I am a trained evolutionary biologist right up until my eight cousins ask me if I would lay down my life for theirs.

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Noah Reid

@NM_Reid

5 years

2) if this is indeed fraud, the only reason it was caught is that the responsible person didn't know how to simulate data. next to becoming a credible expert in a scientific field, getting an academic job, and publishing loads of papers, learning to simulate data in R is TRIVIAL.

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Noah Reid

@NM_Reid

7 years

Completely amazing pine needle mimic at the house this morning.

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Noah Reid

@NM_Reid

4 years

Some suggestions on how to think about what constitutes "low" coverage.

Dr. CG Partridge (@[email protected])

@PartridgeCG

4 years

Is 2X sequencing per sample still considered 'low coverage'?

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Noah Reid

@NM_Reid

6 years

What they claim: simply choosing the most parameterized phylogenetic model available is not risky enough to justify making everyone do intensive model selection. What I think everyone has heard: models don't matter in phylogenetics. wheeeee!

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Noah Reid

@NM_Reid

1 year

I just submitted ~600 17 year old chipmunk Sanger sequences to genbank for a manuscript I thought was long dead, but somehow came back to life and is now accepted for publication... pending accession numbers.

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Noah Reid

@NM_Reid

2 years

GFF has to be the most flouted bioinformatic file format.

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Noah Reid

@NM_Reid

4 years

Has anyone ever done a study on the extent to which savings from bulk purchases at places like costco are offset by increased consumption he thought to himself as he ate 12 strips of dried mango.

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Noah Reid

@NM_Reid

4 years

@mike_c_mahoney I felt terrible when he killed things but when somebody first told me about the toll outdoor cats take on wildlife, like tons of other people I got angry and defensive and rejected it. It sucks when somebody tells you that something you love, and I did love having my cat outdoors

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Noah Reid

@NM_Reid

5 years

It's amazing that biology can be done at this taxonomic and geographic scale now, but I wonder how much credit the 13 museums listed in the acknowledgements of this paper will get for making a paper like this, with only 5 authors, possible.

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Noah Reid

@NM_Reid

7 years

has anyone ever received a GFF file they didn't have to manipulate 100 different ways before they could do a single useful thing with it?

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Noah Reid

@NM_Reid

5 years

Somebody should train a machine learning classifier that can easily alert you when a RAD-seq dataset is hot garbage.

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Noah Reid

@NM_Reid

5 years

@koaleszenz I love how the comparison is "teach someone to do multiplication" vs "watch someone who already knows how".

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Noah Reid

@NM_Reid

4 years

I can't get over that he opens with that shit about delivering babies. personally I don't think anyone deserves the title doctor unless they have stitched together parts of various corpses into a hideous monster and then successfully brought it to life with a bolt of lightning.

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Noah Reid

@NM_Reid

3 years

I love birding, but man I question my choices when I'm thinking about taking some of my precious free time to go to a nail salon parking lot to look at dirty gulls lounging on the roof of a waste transfer station.

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Noah Reid

@NM_Reid

5 years

I really enjoyed the ASN presidential address by @MikeWhitlock63 on scientific methodology. I think his intro on the absurdity of "p < 1e-253" should probably be a shot across the bow for all of us doing genomics stuff. #Evol2019

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Noah Reid

@NM_Reid

6 years

I really like this review. It is extremely accessible for a difficult (to me anyway) topic: Patten, Manus M. "Selfish X chromosomes and speciation." Molecular ecology 27.19 (2018): 3772-3782.

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Noah Reid

@NM_Reid

10 months

"What do you mean you've never heard of the gene ND5!? It was only the third most popular gene used for single-locus mtDNA phylogeography in the 2000s!"

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Noah Reid

@NM_Reid

5 years

I'm not a fan of the commonly seen numerical system for denoting bayes factors. Let's embrace 21st century symbology and do better: k < 1🤔 k = 1🤔 k > 1🤔 k > 10🤔 k > 100🤔

Dave Nelson

@nelson_lab

5 years

I’m not a big fan of the commonly seen *, **, *** system for denoting p-values on graphs. Let’s embrace 21st century symbology and do better: p < 0.1 🤥 p < 0.05 🤔 p < 0.01 🙂 p < 0.001 🤩 p < 0.00000001 🤯

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Noah Reid

@NM_Reid

2 years

I'm feeling completely overwhelmed by all the stuff I have to do, so naturally instead of doing any of it I lubricated my squeaky office chair. It was such a glorious success I'm calling it a day.

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Noah Reid

@NM_Reid

3 years

I've been trying to remember a joke I heard about genome assembly but I can't quite piece it together.

Dra. Kirsten Isabel Verster 🪰🧬🦠

@kirvers

3 years

I told a joke about DNA pero it was CACA

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Noah Reid

@NM_Reid

4 years

Trivial coalescent/variant calling question: GATK docs state "To minimize the chance of missing singletons, we increase the cohort size -- so that singletons themselves have less chance of happening in the first place." But this is false, right?

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Noah Reid

@NM_Reid

2 years

if you're in northeast connecticut, or maybe anywhere in southern new england and you like birds even a little, you should go birding right now. migration over night was exceptional.

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Noah Reid

@NM_Reid

4 years

Maybe I'm just not up on the methods, but I don't understand how the "model-based demographic inference" and the for lack of a better term "oh my selection really seems to very strongly shape genetic diversity" subfields of population genetics coexist.

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Noah Reid

@NM_Reid

4 years

the three phases of statistics whiplash: 1. this impenetrable jargon seems impossibly complicated. 2. ha! this technique is actually stupidly simple! I understand it! 3. it turns out the actual justification for it is 5 solid pages of math that I don't understand at all.

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Noah Reid

@NM_Reid

5 years

Top Mistakes by which PopGen nerds give themselves away all involve parameter names: 1. "No, Ne has nothing to do with the number of individuals in a population." 2. "You're a fool if you interpret 'admixture proportion' as an admixture proportion. 3. "Linkage disequilibrium"

Jacob A Tennessen

@JacobPhD

5 years

The top mistakes by which non-pop-gen folks give themselves away all involve Hardy-Weinberg: 1. Fail to check HW 2. Assume HW violations are biologically meaningful rather than genotype errors 3. Even w/o HW violations, analyze genotype frequencies rather than allele frequencies

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Noah Reid

@NM_Reid

2 years

finding a baby turtle is always an experience

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Noah Reid

@NM_Reid

7 years

Whoah, is this actually a thread on parsimony vs ML/BI in phylogenetics in which people are respectfully discussing the science? I love it.

Professor John R. Hutchinson

@JohnRHutchinson

7 years

Question for my systematics colleagues: at this point in science history, when if ever is it permissible to publish a morphology-based phylogeny (or character-mapping) study using only parsimony not maximum likelihood/similar methods? (can of worms I know)

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Noah Reid

@NM_Reid

4 years

"epistemological carnage"

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Noah Reid

@NM_Reid

4 years

@mike_c_mahoney I grew up with an outdoor cat that I loved. He was calm and affectionate. All the indoor cats I knew were weird and squirrelly and even worse, used nasty litter boxes. I loved watching him prowl outside, and also loved wondering what the hell he was doing out all night.

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Noah Reid

@NM_Reid

6 years

@Graham_Coop you're misinterpreting. this is obviously a circular cladogram showing that earth is the ancestor of the rest of the planets, and that gas gigantism has evolved multiple times.

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Noah Reid

@NM_Reid

4 years

Population geneticists in publications: look at all the cool things you can infer from the SFS! Population geneticists informally to each other: what the hell are all these snps doing in these bins

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Noah Reid

@NM_Reid

6 years

look for my groundbreaking new course in spring 2018: principles of genomic data re-formatting.

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Noah Reid

@NM_Reid

4 years

I am now 100% convinced that if you look in detail at sex determination in even the smallest clade of fish you will discover evolutionary shenanigans.

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Noah Reid

@NM_Reid

4 years

Many of the population geneticists I follow here have openly discussed struggling with factors of two. Have any of you considered reaching out the IHME to counsel them in these trying times?

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Noah Reid

@NM_Reid

5 years

Horrible father that I am, I tricked my six year old into taking a deep breath of this stinky Pycnospatha inflorescence. @uconneeb greenhouse.

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Noah Reid

@NM_Reid

5 years

@LAevolving This is almost certainly because there is a young-ish, non-degenerate sex chromosome with a very large non-recombining region. Divergence between the still largely homologous X and Y (or Z/W) that exceeds population structure drives the signal.

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Noah Reid

@NM_Reid

3 years

If you are two ECR bodies (+ a few babies?), I can't give you advice on how to succeed, but I am happy to share my experience via DM.

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Noah Reid

@NM_Reid

3 years

so what's the bioinformatic model for population genomics with assembled whole genome sequences (vs reference mapping, vcf, etc)? who's figuring that mess out?

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Noah Reid

@NM_Reid

7 years

Casey Dunn on the value of descriptive work in genomics: no one has CRISPR'ed the earth to see if it revolves around the sun. #evol2017

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Noah Reid

@NM_Reid

11 months

@ethanblinck "you see those birds out the window? from a, uh, genetic, uh, perspective, there, uh, probably aren't as many as it looks like there are? what I mean to say is, uh, they've probably got fewer snps than you might guess"

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Noah Reid

@NM_Reid

4 years

Bioinformaticians: Ugh. Noobs use horrible file naming conventions that increase the likelihood of errors and hamper reproducibility. Also bioinformaticians: please update to the latest version of my software package, 3.1.10, which succeeds 3.1.9.

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Noah Reid

@NM_Reid

1 year

Do frogs have weird 3' UTRs? Like generally huge ones? I'm looking at a gene expression dataset for a frog in IGV and every gene has like 4-15kb of coverage at the 3' end. I don't think I've noticed this before.

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Noah Reid

@NM_Reid

5 years

@amanda_dettmer unsolicited recommendation: our dog takes bravecto, and she hasn't had a single tick since. we started b/c she got lyme and anaplasmosis within a month of moving to connecticut.

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Noah Reid

@NM_Reid

3 years

The epic journey of a very particular breed of dog.

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Noah Reid

@NM_Reid

8 years

evolutionary genetics: conceptually amazing free software everywhere, soul-crushing morass of byzantine input formats and control files.

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Noah Reid

@NM_Reid

5 months

is this a hot take? >95% of bioinformatics software installs pretty dang easily.

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Noah Reid

@NM_Reid

2 years

It seems surprising this would be on CRAN, right?

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Noah Reid

@NM_Reid

3 years

@PartridgeCG I think it's supposed to give a candidate a chance to completely collapse from pressure and exhaustion. Or at least, I used it for that once.

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Noah Reid

@NM_Reid

5 years

A 16 hour rollercoaster: Up: new data! spectacular finding! what does it mean?? Cresting: wait, huh, that can't be right Down: OH GOD SAMPLE LABELS ARE SCRAMBLED Bottom: I can't afford to redo this experiment Up: A clear paper trail allows for label deconvolution. ...

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Noah Reid

@NM_Reid

6 years

Me: how did you learn all this Illustrator stuff? @sarahmhird : 10 years.

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Noah Reid

@NM_Reid

4 years

fun fact I just learned about Stacks: the VCF output when using reference mapped data doesn't put the reference allele in REF and the alternate allele in ALT.

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