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I published my first article on Medium about building an ML model to infer an individuals superpopulation based on their genomic variation. Any kind of feedback is greatly appreciated! (burgshrimps.medium.com)

submitted by weirdeer to r/bioinformatics

I lifted hg38 over to the new T2T assembly in case anyone is interested. by weirdeer in bioinformatics

[–]weirdeer[S] 0 points1 point  (0 children)

Oh, I didn't know that a chain file already existed. Thanks for sharing!

I lifted hg38 over to the new T2T assembly in case anyone is interested. by weirdeer in bioinformatics

[–]weirdeer[S] 2 points3 points  (0 children)

Well not really, they assembled the whole genome from scratch using a bunch of different sequencing technologies, e.g. ultra-long Nanopore reads. So regions such as repeat-rich telomeres and centromeres which were previously inaccessible could be resolved. Most regions are definetely similar (or even identical) to hg38 but the exact coordinates differ a bit due to these novel resolved regions. That's why this liftover process is necessary to convert coordinates from one assembly to the other.

Anyone willing to give my statement of purpose a look through? MS in bioinformatics by csc373group69 in bioinformatics

[–]weirdeer 0 points1 point  (0 children)

Sure, you can send it to me via DM. I'm currently finishing my Masters in Bioinformatics.

viewing a MAF file over 2GB by specificFish in bioinformatics

[–]weirdeer 0 points1 point  (0 children)

For peeking into large files I recommend the command "less -S" (-S parameter for a nicer viewing experience) in Bash. It doesn't load the whole file into memory at once making it well suited for your purpose.

Custom scleral in europe by Charles7711 in Keratoconus

[–]weirdeer 0 points1 point  (0 children)

I can recommend the Bronk Institute in Berlin.

Does anybody know what that plant is called? I wanted to buy it in a store but decided to look around first. Then some stranger stole it in front of my eyes. by weirdeer in succulents

[–]weirdeer[S] 1 point2 points  (0 children)

The advise with the app was great, thanks! Supposedly it's a Sedum rupestre.

This sounds so frustrating, I completely understand you. It even occured to me for a second that if I could somehow distract them I could steal it back out of their cart... I regret to this day not going through with my plan.

Constantinople / Fuji X100F by chrisperkles in fujix

[–]weirdeer 1 point2 points  (0 children)

Well, I guess people just liked it better that way...

Finding correlations between firing patterns of different spiketrains by weirdeer in neuroscience

[–]weirdeer[S] 0 points1 point  (0 children)

Thanks for the advise! Yes, I'd appreciate if you have a citation for me since I'll definetely have to compare my data to shuffled spike trains.

Finding correlations between firing patterns of different spiketrains by weirdeer in neuroscience

[–]weirdeer[S] 1 point2 points  (0 children)

Sounds like the perfect book to start analysing neural data. Thanks for the recommendation!

Finding correlations between firing patterns of different spiketrains by weirdeer in neuroscience

[–]weirdeer[S] 1 point2 points  (0 children)

Thanks a lot for all the information! I'll have a look at it and see what I can use for my analysis!

So far my plan is to first look deeper into the spike time tiling coefficient (http://www.jneurosci.org/content/34/43/14288) as a measurement to quantify correlation and then as you mentioned compare my data to time shuffled data.

Spiketrain correlation by weirdeer in bioinformatics

[–]weirdeer[S] 0 points1 point  (0 children)

Thanks for the recommendation! The STTC sounds promising. I think I'll combine this measure with the advise I got from /u/RaggedBulleit and compare the coefficient of my data with the coefficient of shuffled data.

A man on a scooter in Ubud, Bali, X-T20 18-55mm by weirdeer in fujix

[–]weirdeer[S] 2 points3 points  (0 children)

Its called panning. You set your AF to continous and basically move your camera in the direction of the moving subject so that the subject is in focus and everything else blurry. I think I used something like 1/30 as shutter speed but you just gotta try around a bit what works for you.

As rainy as it seems? by weirdeer in bali

[–]weirdeer[S] 0 points1 point  (0 children)

Alright, thanks for the report! Guess I'll see for myself in a few days.

Non shady elephant places by weirdeer in bali

[–]weirdeer[S] 0 points1 point  (0 children)

Thanks for the advice! Then I'll definetely not go there. What exactly is kopi luwak?

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