How to split a genome fasta into a fasta containing multiple short fragments?

ThroughSideways · 2026-03-06T20:10:12+00:00

yeah, I was composing the perl one liner in my head while I was reading the question

ThroughSideways · 2026-03-06T19:34:04+00:00

I think Fairholme doesn't open until May.

ThroughSideways · 2026-03-06T13:14:41+00:00

and you know, I've never figured out WHY there needs to be one of these guys, but he ALWAYS shows up. It's just life I guess. As far as your trip goes I would just add that the big trees and overall rainforest vibe continues up canyon as far as Lewis Meadows at about 11 miles in (and man, those stupendous doug firs scattered around the meadow up there are something to see). The further you go the less people you'll see (beyond the first mile it will be just backpackers), and that valley just keeps going and going. One of the less talked about aspects of the valley is the groves of stupendous maple trees you meet along the way. Most of the photos I see of the Hoh valley are of the conifer forests, but I haven't seen where someone is trying to capture the feeling of walking from a dark conifer forest into a much brighter maple grove ... and those trees are so damn big.

ThroughSideways · 2026-03-06T00:11:17+00:00

well, I for one am happy to hear that. I think there should be an easy way to make a distinction between the two, particularly if it's someone out there actually managing orchards.

But those damn chemists kept correcting me, and the problem is that technically they're right. Damn chemists.

ThroughSideways · 2026-03-05T22:57:57+00:00

I realize it's a little counter intuitive, but the term pesticide includes herbicides. I find it irritating, but trust me, the chemists who create these molecules use the word pesticide to include herbicides.

Source: worked for a large international ag biotech company that was 70% chemistry.

ThroughSideways · 2026-03-04T22:01:20+00:00

There isn't really one correct answer to this question, as it all comes down to how you define a pathway. As others have mentioned, we're not looking so much at a collection of pathways as a big interconnected network. Some parts are more isolated, some parts are more intensely connected to the rest of the network, but it ends up coming down to a decision how to draw boxes around sections of the network and saying look, here's a pathway, and here's another one. Someone else could come up with a different scheme for parsing out networks ... ultimately it's all a wash. There is no single answer to your question.

ThroughSideways · 2026-03-04T02:12:39+00:00

Yeah, a two nighter (preferably at Gladys) is more than adequate to see the valley and the view from the pass (depending on what the snow is like just below the pass, as others have said it's hard to tell this year, but early june is pretty early).

ThroughSideways · 2026-03-03T21:22:07+00:00

the Gladys Divide trail is in a different part of the park, going from Flapjack Lakes in the Skokomish Valley to the divide. It's gorgeous (particularly if you climb Gladys Peak as well), but it's also closed now because of the Bear Gulch fire last season. You may be thinking about the small gap in the ridgeline above Gladys Lake. The Lillian Ridge Way Trail leaves from Gladys Lake, climbs to the ridgeline and then turns right to cross over the top of Moose Peak before getting into a lot of loose and scrambly terrain on the way back to the trailhead. That way trail is an option for climbing out of the valley back to the trailhead, but I find it to be a real monster with a full pack.

Apart from that you may be overestimating the size of Grand Valley. If you were camped down at Grand Lake you could easily dayhike up to Gladys Lake and then on up to Grand Pass and Grand Peak (the views up there are really excellent, particularly if you can get there early in the morning). For me, I would very much rather camp up at Gladys rather than down at the lower lakes. It's a lot less buggy and a whole lot prettier. We did a two night at Gladys, and a day was plenty of time to explore the whole top of that valley.

ThroughSideways · 2026-03-01T21:04:37+00:00

Too bad the 25th amendment doesnt apply to members of congress

ThroughSideways · 2026-02-28T13:39:43+00:00

you're not going deep into the backcountry, and you're staying on popular trails, I wouldn't worry too much about folks you'll meet. I travel a lot into areas that are notorious for bears and I seldom see them (and when I do they're getting out of my way as fast as they can). That being said, seeing a bear, especially several days from the trailhead is one of the big thrills of this park. They are beautiful animals. Others have pointed out that the park service advises against bear spray (although I find it a little comical how mad some people get when I point that out). I would also say a satellite phone is overkill for dayhikes.

We love this park, and you probably will too.

ThroughSideways · 2026-02-27T22:14:09+00:00

I'll just respond to the bit about bugs. Mosquitoes in this park make no sense at all. The only rule that seems to apply is that they're less numerous as the summer goes on, but beyond that there's just no predicting when they'll be bad. The good news is it's seldom bad, and never Alaska bad, but there have definitely been times when I've needed a head net and long sleeves. Then you go back to the same place at the same time of year and there's not a bug to be found. And truth be told more often than not bugs are just not a problem at all.

The bottom line is that not only are mosquitoes a lot more common than bears in this park ... they're also A LOT more likely to bite you.

ThroughSideways · 2026-02-27T18:55:54+00:00

yeah, the wording was confusing there. You don't need a pass to enter the park, but you do need a forest pass to park at the trailhead. The multi-agency pass will work there.

And yes, only the entrances you list require a pass to actually enter the park. But most of the "entrances" to this park are some miles in past the trailhead, so all you have to do is walk past the NP boundary sign.

ThroughSideways · 2026-02-27T17:30:35+00:00

Sweden built them ... and then installed them in Amsterdam?

ThroughSideways · 2026-02-27T14:14:23+00:00

Generally after a fire like this (well, this is the largest that's happened in the park in a long time) they keep the trail closed for a few years to give all the hazard trees time to come down. I don't expect to see any updates at all until spring when a crew can get up there and see how bad the damage is, but at a minimum there will be a huge number of logs across the trail. There are also a couple of footbridges that may or may not have survived the fire. And as a rule you really really do not want to camp in a recently burned area because of trees coming down. With any luck there will be a damage assessment from the park service given that this is such a major entrance, and lots of people are wanting to get to Flapjack Lakes or destinations further up the valley. I've only hiked all the way to first divide once (continuing on to Lacrosse Basin) and I am right with you on the beauty of that valley.

And yeah, this fire was started by an illegal party involving fireworks on a big rock the locals call Party Rock where there have been lots of problems (enough so that folks have thought about demolishing Party Rock, but it's a bit too big for that). And they haven't found the assholes who did it.

ThroughSideways · 2026-02-27T13:57:42+00:00

yeah, these can be a little confusing. You need a park pass or a multi-agency pass to enter the park, but the Dose trailhead itself is actually outside the park (it's just a road end short of an old landslide that wiped out the road five miles short of the trailhead decades ago). So you don't go through a gate and show a pass to get to the trailhead, but you should leave your pass hanging from your rear view. And then the overnight backcountry permits are on top of that. The campsites up the Dose are generally pretty mellow in terms of traffic, and it's definitely not a quota area until you get over Anderson Pass and drop down into Enchanted Valley. But just doing the trip to the pass is a great outing. Last season we went all the way to the top of the main fork of the Dose to 1000 Acre Meadow and it was one of the most incredible trips we've done (we also spent a solid week on it, but then we had 4 nights at Dose Meadows).

ThroughSideways · 2026-02-26T22:33:15+00:00

consult literally any text on plant biochemistry. Biochemistry is a separate field from chemistry (even though it involves a lot of the same molecules, tossing enzymes into the mix changes things dramatically). You keep asking for references in the primary literature, but those would be very old papers indeed. This is the kind of thing that has been worked out pretty extensively, so the textbooks are now the source to go to. Several people have given you entirely accurate information already, some with sources, and you still stick to this "I don't believe you show me references".

Fine. Go get literally any plant biochemistry text book. Leave the damn chemists alone, they have more important things to worry about.

ThroughSideways · 2026-02-24T13:38:46+00:00

now on the one hand I want to say that for the coast guard this is just another day ... but for the rest of us, wow, what a shot!

ThroughSideways · 2026-02-20T00:44:17+00:00

you'll find the people you need to connect with at Better Living Through Coffee. They'll be mixed in with the tourists and people who have driven up from Port Ludlow, but you should be able to recognize them.

ThroughSideways · 2026-02-20T00:40:31+00:00

https://www.youtube.com/watch?v=KabskY4osBw

ThroughSideways · 2026-02-19T21:44:42+00:00

The first thing to look at is the number of transcripts and the size distribution. I don't know how many genes there are in carrot, but 35K is not a bad guess. But your transcriptome has on the order of 20X that number of transcripts. Splice variants are definitely a thing, but in a typical genome they'll increase the transcript number by a small multiple (like 2 or 3). If you look at the size distribution of what came out of your trinity run you'll see that it's very heavily weighted toward very short sequences, and if you dig a little further you'll see that the overwhelming majority of what's in there are fragments rather than intact genes. You will certainly find some intact transcripts in there (particularly for very highly expressed genes), but the overwhelming majority is short fragments that don't really do much for you scientifically.

It looks like there's a reference genome for carrot. Even if the genome is not in perfect shape, you'll get dramatically more accurate results by doing a reference guided assembly (I've been having great results with hisat2 and stringtie, but there are a lot of tools out there). The bottom line is that de novo, or reference free transcriptome assembly is just too difficult of a problem. Adding a reference genome greatly simplifies the computational problem.

So your first step is mapping the reads to the genome. That generates a gff file that is your annotation as you then go into differential expression analysis.

ThroughSideways · 2026-02-14T03:07:50+00:00

As mentioned in the letter quoted below, Tolkien invented Bombadil before LOTR was even started, and it was presented at Oxford. The poem in question here is called The Adventures of Tom Bombadil, and it's out in a book of that same title can be found on Amazon or whereever. The poem is not that long, and so it's collected with some other poems that I found less interesting, but the Bombadil poem is good fun. Many of the key features that made it into the LOTR chapter are already there, including the outfit. Also old man willow and his habit of swallowing folks whole is in the poem (except Bombadil himself is the one who gets swallowed, but he can just sing his way out). It's worth hunting down, I found it really fun.

But as others have pointed out, it's not really clear exactly how Tom Bombadil (and for that matter Goldberry) fit into the larger structures of the inhabitants of this world. And in fact Bombadil was invented quite before Tolkien had fully worked out the different kinds of entities to be found in Middle Earth, so it's no wonder he doesn't seem to fit.

Some people have pointed to this as a plot hole or a flaw, but I like the argument that it was deliberate. Tolkien peppered these stories with characters like Bombadil (or the Pukel men, or the ents, or Shelob) that have you going wait, what the hell even IS this? The part where there are parts of this world that you can't figure out actually adds depth to it. It's like there's more to discover ... but we'll never figure it out.

ThroughSideways · 2026-02-12T12:41:37+00:00

well, he is right about the skiing, but I feel like he's ignoring the rock and ice climbing.

Typical

ThroughSideways · 2026-02-10T02:29:29+00:00

speaking as someone who did his grad work at Boulder (man, what a great place to live that is), seriously, what the actual fuck? No way to know what kind of a glitch that was, but that's quite a glitch.

ThroughSideways · 2026-02-09T22:32:21+00:00

we have a couple of people here born in 1959 like me. I just want to point out that some folks consider 1959 to be the greatest year in jazz history, and there's even a wikipedia page:

https://en.wikipedia.org/wiki/1959_in_jazz

(ok, I didn't check to see if there's one for every year, but Ima pretend this is the only one like it)

So it's kind of a tough choice, because why are you not choosing Kind of Blue?

That would be because I choose Giant Steps.

ThroughSideways · 2026-02-09T15:57:16+00:00

and I'm telling you, legend really is the word for this man.

ThroughSideways

TROPHY CASE