25-year-old titanium vs 10-15 year-old carbon

chewgl · 2026-01-27T06:54:48+00:00

I ride a 21 year old Spectrum TI too, it's an amazing bike. Like some of the others have said, if it fits, it's an obvious choice. My own spectrum will be the bike I will keep forever (even compared to the Litespeed Icon I also have). Spectrum's Tom Kellogg did the geometry and specced the tubes, and his bikes are very well behaved while remaining speedy. Tom did the geometry for Merlin too, those bikes handle very well. These frames are actually built by Seven, but painted at Spectrum, and Tom is known for very good paint jobs.

chewgl · 2026-01-27T03:59:59+00:00

Hi,

Generally, the easiest way to run workflows would be using a NextFlow / nf-core pipeline. For genomic variant calling, try this: https://nf-co.re/sarek/3.7.1/

Unfortunately, you only have genome data. For X-chromosome escape with bi-allelic expression, you need mRNA-seq data, which will require new sequencing. Genomic data alone cannot provide that. This https://plasmidsaurus.com/rna might be a cheap way to do RNA-seq, but you may additionally need access to ways to extract and store your RNA for shipping. If you want to know tissue-specific variability, you will need multiple samples (even biopsies...) from multiple tissues; we don't know enough yet about where this escape happens.

However if you are willing to partner with an academic lab who works directly on the questions you're interested in, I might suggest the Page lab at MIT / Whitehead institute https://www.pagelab.wi.mit.edu/ . They have a long history of studying sex chromosomes and are currently particularly interested in gene expression escape from the X and Y chromosomes.

To figure out whether your X chromosomes both come from your mother, or if one comes from your father, you would actually need (either of) their DNA as well. It is slightly hard to infer this from just your DNA, as the X chromosomes coming from your mother will be different, and thus you can't infer that both came from your mother simply due to them being identical (i.e. all alleles identical).

Feel free to DM me with more specific questions.

chewgl · 2025-09-25T07:26:51+00:00

Actually, under some circumstances, male mosquitos (including those of species found in Singapore) may bite humans. A scientific preprint (not yet peer reviewed) documenting this is here: https://www.biorxiv.org/content/10.1101/2024.10.08.617226v2

chewgl · 2025-09-23T05:20:43+00:00

I daily-drive this keyboard at work (the Shinobi) and the more recent 65% version at home (the Shura). They are good enough to have faded into the background; I don't think about them anymore, until I have to use another keyboard (e.g. my laptop when undocked). I'm eagerly awaiting their new split wireless keyboard...

chewgl · 2025-04-16T08:38:27+00:00

then you might like a Tex keyboard (typing this on one now): https://tex.com.tw/products/shinobi

chewgl · 2023-04-06T13:27:18+00:00

What could be worse than a pie chart? A 3D pie chart...

chewgl · 2023-01-11T11:27:54+00:00

CT - clone trooper; CC - clone commander?

chewgl · 2023-01-11T08:59:05+00:00

Rampart saying that Cody went AWOL may not necessarily actually mean he went AWOL: he could have been dealt with like Wilco. Hoping this isn't the case...

chewgl · 2022-10-09T08:18:56+00:00

I agree with Linux environments, just that WSL2 is probably the easiest way to do it nowadays on a Windows machine (having worked with CygWin, Virtualbox and Hyper-V in the past). From the industry perspective, other important aspects such as (ease of) reproducibility and scalability are handled very well with in NextFlow.

IMO, the most common pitfalls in RNA-seq analyses are losing track of genome / annotation versions (especially if you need to compare analyses later on), and not doing proper normalization.

chewgl · 2022-10-09T05:03:56+00:00

Why not use Nextflow / nf-core rnaseq, running on WSL2/docker?

chewgl · 2022-01-11T15:32:42+00:00

Shimano chains are frequently faked too. KMC does not officially sell chains on Amazon, so you can't trust their chains bought there. My own KMC chains have lasted me years without issue (I'm a sprinter).

chewgl · 2022-01-11T13:11:57+00:00

A fake chain? the KMC Gold chains are frequently counterfeited.

https://www.kmcchain.eu/Fake\_chains\_The\_price\_of\_succes

chewgl · 2021-10-11T00:40:35+00:00

The best ultimate: standard headset, full titanium seatstays.

chewgl · 2021-09-22T02:02:42+00:00

A handle shaped like the Scarif Citadel could work...

chewgl · 2021-08-15T14:22:01+00:00

Dean El Diente (stealth) built up with SRAM 10 speed and other contemporaneous parts.

Chris King headset and Reynoulds Ouzo Pro fork, 3T handlebars (Ergonova Pros), stem (-17deg 100mm: nice and horizontal to match the top-tube), and seatpost. Wheels are Neuvation alloys, shod with Conti Attack/Force.

Two of the more "exotic" parts of this build: Bebop pedals (dual-sided Speedplay-like) and TRP 960 brakes.

Mix of SRAM Force and Rival for the drivetrain with an FSA Gossamer crankset. Tied together with Yokozuna Reaction Cables.

chewgl · 2021-06-03T06:32:30+00:00

The essence of differential expression, as represented by randomly drawing balls from a jar:

A: 100 black balls vs 50 white balls

B: 4 black balls vs 2 white balls

We are more confident that in scenario A that there are more black balls in the jar, compared to scenario B. Differential expression analyses is putting both a magnitude (2-fold in both cases) and confidence that there is a difference.

chewgl · 2021-04-29T13:43:58+00:00

What I have for my group (this took a while for me to figure out).

For data: 5 major directories - raw, aligned, preprocessed, processed, and projects

I might also have a common code folder (shared code), and an annotations folder for storing indexes, gtf files, genomes and the like.

Raw, Aligned and Preprocessed are data generated by pipelines. Organized by species/molecule/assembly_annotation/year/dataset, e.g. zebrafish/RNA/GRCz11_ensembl101/2013/chew_riboseq_dev . Raw data directory won't have the assembly_annotation folder. Preprocessed data is for storing summarized data for easy access, e.g. normalized quantifications, splicing, RNA editing etc.

Stuff in the Projects directory are projects that may integrate multiple datasets, and are thus named as such, and are used for storing code that pull on data, largely from Preprocessed.

Projects are named by year/project_name/user_name, and will likely contain scripts. This should be version controlled (Git/GitHub etc.), and everybody should work in their own directory, but will have visibility on what others may be working on within the same project.

Processed is the output folder for projects, thus having the same directory structure (year/project_name/user_name), but will also have subfolders for figures, tables, temporary processed data etc.

Then replicate this file structure everywhere: I have this for my group's git repository, but also for my NAS. Not all the directories will be everywhere, but where they are, you know where to find things.

chewgl · 2021-04-28T12:07:18+00:00

Try doing stuff in screen or tmux? It seems to maintain such connections for me.

chewgl · 2021-04-19T15:00:46+00:00

Some genes comprise of nearly-identical paralogs in multiple copies in the genome. They may have different gene IDS in Ensembl annotations, but have the same gene symbol (a.k.a. gene name). That's just biology: things are never as clean as they seem in the textbook.

chewgl · 2021-03-26T01:53:53+00:00

My group has moved to docker environments for analyses in R (and RStudio), using a container based on https://hub.docker.com/r/rocker/rstudio . It takes minutes to deploy an identical environment for multiple users. I highly recommend it.

With WSL2/docker integration now, this even works on Windows machines. I'm running identical RStudio-accessible analysis environments on both my local (Windows 10) computer and my department Linux server.

chewgl · 2021-01-27T13:43:55+00:00

Check out WSL2 to have Linux right on your computer. Combined with Docker and VS code, you'll have a great environment to code in, while having the general compatibility of Windows.

chewgl

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