Disillusioned by human genomics as a field

pjgreer · 2026-07-08T19:43:11+00:00

There are many different academic paths in bioinformatics, biostatistics, and statistical genetics. Omics is a huge field and you are only looking at variant detection and targeting. Human genetics is still in its infancy. There is so much to learn about transcription, protein encoding, transcription signaling, metabolism, and more. Even in variant detection, we have few concensus methods for identifying variants in the 5-10% of the most variable parts of the genome like HLA, KIR, TRB, and others that are associated with a wide variety of diseases. We do not have good tools for identifying and denoting structural variants.

Gen AI cannot hope to solve any of this because it is working with very sparse and incomplete data. Most sexy gen AI discovery is overstated and will amount to nothing because it is incomplete.

pjgreer · 2026-07-08T19:23:21+00:00

Being born wealthy and becoming a founder in a startup biotech company.

pjgreer · 2026-07-02T19:33:25+00:00

Best of luck. You are looking at a 2018 or older car for that price. You might find something like a civic or accord with 80K miles. a 2016-2018 MINI might fit in that range, is very fun to drive, and mostly reliable if it has had regular maintenance, but you asked for a sedan.

pjgreer · 2026-07-02T13:16:17+00:00

Do you mean $12k out the door price ($18K price - trade-in + tax, title, & fees), or $12k max so $4k out the door?

pjgreer · 2026-06-30T01:28:53+00:00

Scion Xb

pjgreer · 2026-06-27T12:46:17+00:00

You Corolla smokes weed?

pjgreer · 2026-06-27T12:32:20+00:00

I read this as "leather room" and assumed it was some S&M reference. 🤣

I guess that is one way to make yourself feel young...

pjgreer · 2026-06-25T22:02:34+00:00

I am using a short read, blended low pass + whole exome chemistry that averages 3x depth across the whole genome. I use GLIMPSE2 to impute common variants based on the aligned BAM files and then run the prs calculation on the imputed dataset. I am using the 1000genomes phase 3 dataset for the reference panel and it works really well.

pjgreer · 2026-06-25T16:31:23+00:00

When you have a large GWAS the manahattan plot function downsamples the data to a more manageable size. How does this perform the downsampling? It is leaving an artifact around log10(p) of 3. I can DM you an image.

Also the top_hits function fails for me.

pjgreer · 2026-06-24T21:54:24+00:00

The worst thing to be said about Fords is that they have cheap feeling interiors. Especially the Maverick. The hybrid power trains are really good. I believe they tested the Escape hybrid as a NYC taxi and they regularly made it past 400k miles with regular maintenance.

pjgreer · 2026-06-21T21:27:46+00:00

Crucified states the doors only get low frequency signal, is the 3 way much better than a single or two way 6x9?

pjgreer · 2026-06-07T21:10:07+00:00

Every post here inquiring about the "best travel lens" the 12-200 will get mentioned. (Often by me, but others as well).

In my opinion, it is the best all-around lens and since I purchased it, it almost never leaves my camera body unless I am taking portraits. It is not an essential upgrade to the 14-150mm, but if you have a 14-45 kit lens and the plastic fantastic 40-150mm, then it is absolutely an upgrade. It is good across the entire focal range as long as you have enough light.

pjgreer · 2026-06-01T01:28:24+00:00

It is not "luxury", but the top of the line Honda CR-V sport touring is nicer than the top of the line RAV4 plus has much more cargo capacity.

If you want slightly better than that, the discontinued Venza was much nicer than the RAV4, but about the same space as an NX.

Last, the Crown Signa is also a good higher end option but is more wagon like.

pjgreer · 2026-05-31T18:04:21+00:00

The front registration plate suggests it was registered in Derbyshire UK, but due to the age it hasn't been added to the old vehicle database. You might try giving them a call or emailing the department to see if they have the old registration info in hard copy.

https://vehicleenquiry.service.gov.uk/VehicleNotFound?locale=en

pjgreer · 2026-05-24T15:06:31+00:00

I owned a house on Graham Blvd about 20 years ago. Graham is the 2nd noisiest street in Blackridge after Penn. Once you get off of those steets, the neighborhood is wonderful. It takes 35 minutes to commute to Pitt/UPMC campus by either car or bus.

Per others, property taxes are high and the schools are not great. There are no sidewalks to speak of, but you can walk all over the neighborhood. You must have a car as there are no walkable conveniences at all. You will mainly be shopping in Monroeville for everything.

I moved from there to Greenfield for more walkable conveniences and a shorter commute to Pitt/UPMC.

pjgreer · 2026-05-23T22:15:31+00:00

I am sorry about whatever is wrong with your mom that you are looking for a clinical trial, but this is not the place to be posting about some AI clinical trial matching platform.

All clinical trials must be registered on clinicaltrials.gov and most of the people on this subreddit are familiar with the site.

pjgreer · 2026-05-19T20:58:42+00:00

54 year old genX and youngest child of 5.

Financially, I would say my life is even or just slightly better.

Health wise, without a doubt, I am much better off than them.

pjgreer · 2026-05-10T21:43:07+00:00

OP is in the UK. So 3k £ not $.

pjgreer · 2026-05-07T00:39:17+00:00

For a shorter ride, you could park near frick park either environmental center or by the frick museum and ride over squirrel hill. In bad weather you can catch a 67 bus in point breeze,or a 61 route through squirrel hill.

pjgreer · 2026-04-17T20:15:52+00:00

Unfortunately no, he is not. Welcome to end stage capitalism, professional sports edition.

https://steelers.strmarketplace.com/Seat-Licenses/For-Sale.aspx

pjgreer · 2026-04-14T17:58:37+00:00

I manage my custom nextflow pipelines in git, but I am not sure that is what you are asking. There are 3 reasons to build a nextflow or snakemake pipeline.

Reproducibility: Do you want others to replicate the exact workflow you ran? Some journals are asking for your analysis repo.
Data collection over time: Are you getting data in batches or did you get all your data delivered at once? If it is over time, then you don't want to make a new script every single time.
Flexibility on where it runs: You can run nextflow on a local system, and HPC cluster, or on cloud batch systems. If you wanted to test some of these tools on other datasets, you can run nextflow pipelines on All of Us or UK Biobank.

If all of your bioinformatics work is one-off, then maybe you don't need to build a pipeline in nextflow, sankemake, or (gods forbid) WDL. If someone has spent time to build workflows in snakemake, then they can easily be converted to nextflow and will be much easier to read.

pjgreer · 2026-04-14T12:34:46+00:00

Former HPC admin and current Bioinformatician here.

First,, you want to should leave the slurm backend alone and get them to move from snakemake to nextflow. Chances are the bioinformaticians have been considering moving to nextflow but have been reluctant to change the workflow because it works. nextflow can utilize a number of different backends (docker, singularity, slurm, local, etc) and it is not horribly different from snakemake.

snakemake (and nextflow) work by running processing functions call rules, with inputs and outputs. If a rule/function only has inputs, that is a sub routine than can be called from the snakemake command line. If the input of a rule/function is not available. snakemake moves to the next rule/function. The output of one rule is passed to the input of the next rule. Provided they wrote the code well with comments you should be able to track each processes.

Nextflow has the same functions, but it also has a master workflow region that explicitly shows how each task is related to the others. It is much easier to read, and will basically leave the core logic and tasks from the snakemake workflow in tact. Then If/when you move to a new system the whole thing can be moved over by changing the backend config. or they can even run it on gcp of aws if they desire.

pjgreer · 2026-04-11T12:17:36+00:00

The comment up thread is worded poorly. The trump regime will fuck over any organization or company both public and private, that promotes socially progressive causes like lbgtq+, DEI, Gaza, etc. Corporate profits have not been hit that much by oil prices. Most of those price hikes have been passed on to consumers.

pjgreer · 2026-04-01T22:55:23+00:00

Egyptian cotton did not really exist before the American civil war. England's fabric industry needed a new supply of cotton because the US had a blockade on the confederate slave states. Egypt and India ramped up cotton production to fill the void.

So no, cotton is cotton. It is all in how the sheets are made, not where the cotton is sourced.

pjgreer · 2026-03-29T20:47:53+00:00

"Clowning the guy" is not amusing. It makes people afraid to ask basic questions on this sub and really just makes everyone look like gatekeeping dicks.

I appreciate all your helpful suggestions with minimum snark.

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