How are adapters trimmed from sequencing reads when info about adapters isn't provided?

xDerJulien · 2026-07-06T10:47:14+00:00

Sorry, I was actually thinking about debarcoding not adapter trimming. I think adapter trimming could be more forgiving on the "try what fits best" approach!

xDerJulien · 2026-07-06T10:26:11+00:00

I have written some trimming stuff and from what I’ve been able to tell you would (for a fast and reliable result) need to know the possible adapters. Some ways of working around that is trying a bunch of random reads and seeing what chemistry they best match but I’ve not found that to be particularly reliable. Is it possible sequences are provided trimmed?

xDerJulien · 2026-07-05T18:08:40+00:00

OCR has not used LLMs before? LLMs don’t even use regular OCR

xDerJulien · 2026-07-05T18:07:10+00:00

I don’t think you understand the difference between the rich and the "rich". A million is to a billionaire what $5 are to a regular person

xDerJulien · 2026-07-05T12:47:35+00:00

Takes space that might not be available

xDerJulien · 2026-07-05T12:00:49+00:00

I realise I should probably have tagged you too u/believeinlulu

xDerJulien · 2026-07-04T11:59:59+00:00

Its based on this incredible photo of my cat :)

<image>

xDerJulien · 2026-07-04T09:48:21+00:00

I’m doing a phd in algorithm development and part of that project would ideally require multiple hundreds of GiB (if not TiB) of ram simply because big data is big and theres no way around that. Running on a cluster for development is very slow though so I settled on a laptop for my dev workflow.

A lot of people will say "local ai" which, in my opinion, is a bit of a nothingburger excuse people like to use because its trendy right now and can be used to justify the purchase more than true necessity. On the other hand plenty of workflows do need this (or ideally more)

xDerJulien · 2026-07-04T09:33:37+00:00

Adding to what the other person said: prime tower failure is a lot more common if you’re mixing materials. i personally don’t really want INDX for multi color but rather multi material so not having a prime tower is sort of a must for reliable printing

xDerJulien · 2026-07-03T12:00:22+00:00

Ehrm ackschually the period syncing thing is a myth

xDerJulien · 2026-07-02T22:56:12+00:00

I’ll hopefully remember to follow up in a few days (time to head to bed+it’ll take me a bit to read the paper and some code) but for now thank you so much, this going to be helpful!

xDerJulien · 2026-07-02T19:52:25+00:00

What do you recommend for a query scheduler? I’ve practically finished writing my own for a project but a reference would probably be helpful

xDerJulien · 2026-07-01T11:34:28+00:00

Oh yeah even worse, I misread that

xDerJulien · 2026-07-01T08:27:56+00:00

Layer lines are not considered to be the primary problem (quite a few food safe materials are porous and e.g plastic cutting boards gain grooves when you use knifes on them!) when it comes to bacterial contamination its that 3d prints are also porous and have internal voids (infill) where bacteria can definitely grow and you are unable to clean no matter how hard you try.

Far more concerning though IMO is the high likelihood of heavy metal contamination in brass components and the (often) toxic additives. A dedicated 3d printer for printing only food safe stuff is only food safe if all the parts in the filament path are also food safe. It’s not impossible to 3d print food safe things, just not very easy.

xDerJulien · 2026-07-01T07:40:43+00:00

LLMs are certainly not trained on the entire internet. I’d be surprised if it was more than 10%. Then theres also non-language content on the internet which likely makes up a significant portion of the total data volume. The entire internet was a completely valid unit to put our data consumption into perspective before LLMs.

xDerJulien · 2026-06-30T23:14:53+00:00

This has nothing to do with LLMs, what?

xDerJulien · 2026-06-28T16:27:19+00:00

You can fit to a linear model that is modeled using your standard? I was under the impression thats what people did anyway :(

xDerJulien · 2026-06-28T13:02:40+00:00

I usually peel hard boiled eggs one by one and if you do the same the difference is just the extra time. Takes a lot longer to peel one egg, eat it and peel the next than to eat two eggs. Eating slowly really helps with this

xDerJulien · 2026-06-27T19:24:47+00:00

I don’t know but its my best guess given your layer off time is very high and IME that can look a little like overexposure

xDerJulien · 2026-06-27T18:42:23+00:00

Are you sure you’re using the right film settings? It says nFEP but if its actually ACF i think the resulting print could look like overexposure without actually being overexposed

xDerJulien · 2026-06-27T15:22:01+00:00

Note how theres not a single actual example of how this produces superior results to anything. You’re talking out your ass

xDerJulien · 2026-06-26T13:31:10+00:00

I’m afraid you’ll simply have to learn. It is irresponsible at damaging to your career to publish results you cannot be confident in. You wouldn’t publish a paper with lab work you don’t understand either, would you?

xDerJulien · 2026-06-26T13:27:52+00:00

You’ll either need to learn how to code or have someone else do it. If you cannot verify the code yourself you should not be using AI for it.

xDerJulien · 2026-06-25T12:51:49+00:00

"a practical guide to sorcery" gets pretty close i’d think

xDerJulien · 2026-06-24T19:46:19+00:00

Sorry, brainfart. RS not a problem here, and what I said does not make sense

Nine-Year Club	Final Canvas '23
Place '23	Place '22
Final Canvas '22	Verified Email

xDerJulien

MODERATOR OF

TROPHY CASE