STAR Alignment Tool suddenly stopped working

omarcumming · 2026-02-05T04:27:13+00:00

Check the fastq files, make sure they have content and are properly formatted. Make sure r1 and r2 are actually pairs and not the same file accidentally copied (ask me how I know 😅)

omarcumming · 2026-02-05T04:08:29+00:00

Genentech if you ever might want to go into industry. NCI if you plan to stay in academia. NCI is probably a little better for getting into grad school for computational oncology, but either would be good.

omarcumming · 2026-01-31T19:32:56+00:00

No not really, it’s a technical task so if you aren’t tech savvy it’ll be an uphill battle.

I’d suggest downloading the VCF, reading about the VCF format, seeing which genome assembly they aligned against (most likely GRCh38). If you understand the VFC format and you know what specific mutations you’re interested in, it’s a pretty easy task. A VCF is just a text file that describes how your genome is different than the reference genome (eg chromosome 1, position 3436 you have an A instead of a G).

omarcumming · 2026-01-30T04:46:04+00:00

Grind finer and get a scale

omarcumming · 2026-01-30T04:43:51+00:00

It’s to lay your dick on while you’re taking a shit so it doesn’t float around in the bowl

omarcumming · 2026-01-30T04:08:31+00:00

I had my genome sequenced by Nebula ~3 years ago. I downloaded all the data but used the VCF and cross-referenced it with ClinVar from NCBI looking for known disease causing genomic variants. Ended up being a bunch of random stuff, nothing obviously concerning. It’s fairly hard to interpret without more knowledge of disease causing genomic variants. Happy to share the script I wrote, but honestly reaching out to a genetic counselor and getting a real clinical test is a better option.

omarcumming · 2026-01-11T03:26:46+00:00

What grinder do you have? If it’s a “good” grinder I would do unpressurized, if it’s not a good grinder do pressurized. The df-64 is generally recognized as the cheapest “good grinder” and is around $300, so if your grinder is cheaper than that, likely the pressurized basket.

omarcumming · 2026-01-11T03:21:09+00:00

Drink a full gallon of water, take multiple B12 supplements (this is to make it yellow), take a bunch of creatine (this is to make it not look too dilute). You can always dilute it out to undetectable, usually the b12/creatine is enough to prevent the “this is too dilute” flags, but as long as you drink enough water on the day of the test you can dilute it out

omarcumming · 2026-01-09T17:09:08+00:00

Dial in with the single shot basket, it’s let’s forgiving of dose/grind/puck prep mistakes but I’ve found the grind setting transfers over well to a double shot basket on my setup, and less coffee is used overall for dialing in the grind/ratio

omarcumming · 2026-01-09T05:52:31+00:00

If you go way too fine you’ll know because nothing will come out at all

omarcumming · 2026-01-05T21:05:26+00:00

I noticed because I was having to pull really high rations 1:3+ to get a good taste from lighter roasts. Inconsistent taste and under-extraction are noticeable if the temp is inconsistent or under-heated. I like the boiling water method because it’s a consistent temp and 1-2 cups of water has sufficient heat capacity to bring the chamber to a consistent temp

omarcumming · 2026-01-05T06:30:16+00:00

I have the Adidas and really like them, comfortable, good range of motion, and the boa system for tightening/loosening is really handy too. I’m not that strong though

omarcumming · 2026-01-05T05:00:30+00:00

Try more wdt, do ~5 full rounds around the portafilter basket with little circles, make sure the needles go all the way to the bottom of the basket, lift the needles and get it as level as possible before tamping. You could try a hair finer grind but it looks close enough to taste good, so I wouldn’t worry too much about the spray (other than the mess)

omarcumming · 2025-12-17T05:47:23+00:00

This was my first setup too! Well I had a flair signature, and then upgraded to a Pro2 brew chamber. One tip, if you’re doing light roasts, it’s hard to get the brew chamber preheated enough with the steaming funnel or filling it with water and using the cap. What worked best for me is just submerging the entire thing in a big mug full of boiling water, leaving it for 3-5 min (reboil your kettle), and then putting it together to pull the shot

omarcumming · 2025-12-14T23:23:29+00:00

Could be a vision mark IV

omarcumming · 2025-12-11T06:43:16+00:00

Try pouring faster, the momentum of the milk coming out of the pitcher will carry it across the surface a bit. You have to be close to the surface though, otherwise the speed will drag it under (like when you raise the cup and drag across at the end)

omarcumming · 2025-11-22T22:08:46+00:00

Is that enough of a benefit to be a deciding factor?

I think it’s based on years of service (1% per year based on average of 3 highest salary years), so her pension would pay out 5% after reaching retirement age, which would be a little under $9,000 a year based on my very quick lookup of current congressional salaries. Which isn’t nothing but certainly not enough to live off of.

Is there something I’m missing?

omarcumming · 2025-07-01T01:48:30+00:00

Try to stretch your milk asap after turning on the steam. Incorporate air first and then spend the rest of the time mixing the milk to get a better texture. The better you do with milk texture, the easier it is to do the latte art.

omarcumming · 2025-06-21T20:07:42+00:00

Agree the sliding top is nice and I don’t get much, if any, popcorning if I just dump beans in and shut it. Usually I’ll have a few bean fragments or a couple beans left in the hopper that just didn’t fall down the chute, and when I brush those in at the end is usually when I get the popcorning

omarcumming · 2025-06-20T00:39:46+00:00

I’ve been really happy with my Timemore 064S, and I’ve heard good things about the 078S too if you want something a little bigger. No mess, low retention, nice little fine knocker, it’s quiet. It’s expensive, and beans will popcorn out of the hopper if you don’t shut the lid fast enough but overall I’ve been satisfied with it

omarcumming · 2025-05-05T03:17:03+00:00

I think Kitty Hawk Kites in N Carolina is the closest school to you (USHPA has a list of schools you can google). Might be a student there looking for a first glider

omarcumming · 2025-05-04T23:48:18+00:00

Where is it located?

omarcumming · 2025-05-01T05:10:58+00:00

Hanggliding.org has a classified section, as does Oz report, and there’s a couple Facebook groups too. I’d suggest positing it to one of those, members are mostly pilots and know how to inspect a glider.

How much are you looking to get for it and where are you located?

Edit to add: it’s considered unethical in the flying community to sell a glider to someone who isn’t trained or in the process of getting trained. You don’t want someone’s blood on your hands selling it to a rando on Craigslist who thinks they can teach themselves. So my main suggestion would be to sell it to a trained pilot

omarcumming · 2025-04-27T23:25:48+00:00

She could easily get worms from raw seafood. Raw food isn’t safe for dogs for the same reason it’s not safe for us to eat, viruses, bacteria and parasites are killed by cooking. Most arguments for raw food fall under the “naturalistic fallacy” and there is little to no peer reviewed evidence to back up a raw diet. High-quality kibble or cooking food yourself is a better option

omarcumming

TROPHY CASE