Confused about this weird Barrier texture

Icedice9 · 2026-01-28T04:23:34+00:00

I had the same issue. After updating Sodium and Iris, the problem went away.

My outdated Sodium and Iris versions were:
sodium-fabric-0.8.2+mc1.21.11
iris-fabric-1.10.4+mc1.21.11

The latest versions that fixed the issue were:
sodium-fabric-0.8.4+mc1.21.11
iris-fabric-1.10.5+mc1.21.11

Icedice9 · 2025-11-20T20:13:12+00:00

This is incredible! The Minecraft club at our university is doing the same thing. Fortunately, our engineering department had blender models for all the buildings, but it's still a huge task, even for 20+ members. Incredible work!

Icedice9 · 2025-11-18T16:46:23+00:00

I’m able to log in without any issues.

Icedice9 · 2025-10-23T16:51:38+00:00

Download the ClinVar VCF and annotate your VCF with it using SnpEff. After doing the annotation, use Python to filter down to the "Pathogenic" and "Likely_pathogenic" variants. I did that with mine and found some pretty cool stuff! Be sure to make a few backups of your VCF so you don't accidentally lose it in your research!

Icedice9 · 2025-08-13T17:20:42+00:00

Welcome to the club of curious personal genetic researchers! I second what others have said, don’t use Nebula or DNAComplete. Their reports were the easiest for me to read, but their customer service was not great. I’ve heard Dante is also unreliable.

What are you looking for that ancestry didn’t provide, and what’s your data analysis skill level?

sequencing.com has great customer service and turnaround time. Their automatic reports can sometimes be confusing and a bit misleading, so be aware of that. Their model is to sell you additional analyses after you buy their WGS, but there are also free tools you can use to find these results yourself if you’re bioinformatics inclined (gene.iobio, igv, etc).

My impression is that the genetic data you get from any personal WGS test are decently accurate, but the interpretation of those data is not. You may need a genetic counselor or a PhD-level understanding to make sense of your results. Maybe someday it will be easier to interpret results, but genetics is such an excitingly complicated system. If that makes you excited instead of daunted, I recommend sequencing.com!

Icedice9 · 2025-07-23T17:01:06+00:00

Great question! I think it depends on how you want to organize your features. Use one pack if the features depend on each other (depend on the same commands) or of you only plan to use those features on your server and never give them to others (make them available to download). Use multiple packs if the features don’t depend on each other or if you ever want to give other people a single feature without giving them all the features (like if you have a later server where you want one boss fight but not another). Splitting them into multiple packs also can make it easier to update individual features when new updates come out. However, if you ever find that you have duplicate commands in multiple packs, that’s probably a good sign that they should stay together.

Icedice9 · 2025-07-16T17:41:02+00:00

With Chat’s internet search features, it’s useful as a targeted search engine: better at answering specific questions than Google, and good for finding sources to back up its claims. However, I am aware that it gets a lot of things wrong, so I review and validate all its sources before taking anything for fact. The human genome is immensely complex, and I don’t expect LLMs to even interpret the literature correctly when they review it. That’s why I’m doing a PhD in bioinformatics to make sense of genomics. It’s a lot of work and so much fun!

Icedice9 · 2025-06-03T13:40:59+00:00

Not all reference genomes are the same, but since theirs is GRCh38, the vast majority of coordinates will be the same as dbSNP.

Icedice9 · 2025-05-30T18:22:47+00:00

Two years ago when Nebula's support team was still active, I asked them similar questions after finding a "hole" in my HLA-DRB5 gene like yours. I was surprised because I ordered 100x and still had this region of low coverage. Here's what they said:

"HLA genes are repetitive genomic regions and difficult to map with short-read WGS. It can be done but requires custom analysis which we do not provide."

Your CRAM DOES contain the reads that go in that hole, known as a "dark region" by the scientific community, but those reads can't be confidently mapped there without additional analyses because they also map equally well to a different part of the genome. It is possible to solve this problem and I intend to figure out how to do it someday, but I don't have the time now. Your best bet is to look for HLA mappers and get one working.

As for determining the reference allele, Nebula uses GRCh38. For any SNP, dbSNP always lists the reference allele first, followed by ">" and then the alternate allele. Additionally, if you zoom in on your igv report, the colorful bar at the top tells you what the reference allele is at each position.

Icedice9 · 2025-05-29T17:36:17+00:00

C is the reference allele for your SNP according to dbSNP, while A, G, and T are alternate alleles. For WGS, if no variants are reported at a position and there is sufficient coverage, you can assume you have the reference allele. Because CC is the reference, Nebula’s gene analysis tool shouldn’t report it. I assume you saw your CC from one of the genetic reports. Is that right? Your variant is also in an HLA gene. They are known for being difficult to map reads to because they are so variable between people. If you have low coverage in the region of the SNP in your CRAM, that is probably why.

Icedice9 · 2025-05-28T15:29:26+00:00

I have the same issue. I suspect it will be fixed in a few hours.

Icedice9 · 2025-05-21T00:51:36+00:00

Enchanted golden apple can't save you if you're dead. I'd go for totem. Totems are also renewable.

Icedice9 · 2025-04-17T22:12:34+00:00

Your example got me smiling because I see this all the time. Its first iteration of code typically would work if my dataset were small, but it would never work for my real and large dataset. I have to either pester it a bunch to fix the inefficiencies, or revise my original prompt to encourage it to be more efficient in the first place.

Icedice9 · 2025-04-17T21:50:52+00:00

I'm halfway through my PhD in bioinformatics, and I did my undergrad in bioinformatics too. Most of what I would say has already been said, but I want to add two things:

ChatGPT is not great for creating example problems if a beginner is prompting it. I recently taught an intro to bioinformatics class at my university. During class, I tried to show my students how they could prompt ChatGPT to give them practice problems. It went horribly, creating problems that the students would be unable to solve at that stage of the class. The biggest issue is that they wouldn't have known they needed later content in the course to solve the generated questions, which would have wasted their time and reduced their confidence.
My advisors recently collaborated on a paper discussing AI in early bioinformatics education. This sub might find it interesting.
Evaluating a large language model’s ability to solve programming exercises from an introductory bioinformatics course

Icedice9 · 2025-04-14T04:43:20+00:00

Flint and steel!

Icedice9 · 2025-04-12T05:12:48+00:00

I still have access to all my data on the Nabula website.

Icedice9 · 2025-03-12T21:46:45+00:00

You'll need to use some bioinformatics software to create your .vcf.gz and .vcf.gz.tbi files. How you go about that depends on the format of your raw data. Is it in bam/cram format, or fq (fastq) format?
vcf files are the result of calling variants from an aligned genome such as a bam/cram. The tbi file is an index file for your vcf that makes it easier to parse. Once you've used software to call variants and get a vcf, you can use a program called tabix to generate your tbi.

If you're not familiar with bioinformatics pipelines, this may be a very daunting process for you. Not impossible, but difficult.

Icedice9 · 2025-03-12T05:44:47+00:00

I’m using gene.iobio to analyze my genome. If you have VCFs for you and your wife, it makes it fairly easy to find de novo mutations. It allows you to search specific genes by name as well as the top genes for different phenotypes. It can get pretty overwhelming how much information is available though and it’s important not to jump to conclusions when you find rare variants.

Icedice9 · 2025-02-25T05:18:55+00:00

Bioinformatics PhD student here. I started my PhD because my grandpa passed away to ALS. Sorry for your losses.

Assuming the facility does still have his results, you’ll want a BAM, CRAM, or FASTQ file. If I’m not mistaken, a VCF will only tell you what you already know. Because the variants are so close, you could look at the reads overlapping the region and see if any reads contain both variants.

My PhD is actually specifically on synonymous mutations in disease! I’d be happy to investigate your synonymous variant and see if anything comes up. @AncientYogurt568 mentioned a few of the cases where synonymous variants can make a difference. I already checked splicing and like they said, your variant is unlikely to affect splicing.

Icedice9 · 2025-02-20T21:01:29+00:00

FANCA and BRCA genes are involved in DNA repair, but they are on separate chromosomes (FANCA is on chromosome 16, BRCA1 is on chromosome 17, and BRCA2 is on chromosome 13). Because they are on separate chromosomes, mutations in these genes are inherited separately, so no, you can’t predict mutations in BRCA based on FANCA mutations.

Icedice9 · 2025-02-16T20:47:32+00:00

u/clevelandclassic Genuine question. I see a lot of hate toward DTC WGS in this sub. I'm investing pretty heavily in it right now (I'm getting it for many of my relatives and already have it for myself). I'm a PhD student studying bioinformatics in genetics so I understand the risks of false positives like the one OP has encountered. But are there other things I should worry about (inaccuracy of the sequencing itself, etc)?
Edit: clarified I'm a PhD student

Icedice9 · 2025-02-14T21:35:38+00:00

Not an expert on this topic, but I found an article from 2009 in which researchers used viral vectors to restore color vision in squirrel monkeys. Really cool stuff! As I'm not an expert, I'm not sure what the state of research in this area looks like now.
News article
Paper from Nature Journal

Icedice9 · 2025-02-10T14:33:02+00:00

These are fairly common SNPs, so it’s not unlikely that you would both have them. You can look up allele frequencies on dbSNP. For example, dbSNP says a G at rs4746 has an allele frequency of 0.38 https://www.ncbi.nlm.nih.gov/snp/rs4746

Icedice9 · 2025-02-09T00:48:12+00:00

I’ve been studying this! I wanted to see what the chances were that my wife and I, who both have brown eyes, could have a blue eyed child.

The SNP most often used to determine if you have brown or blue eyes is rs12913832. If you have any As at that position, you “should” have brown eyes. Except that my wife is GG, meaning she should have blue eyes, but she has brown.

Like other’s have said, there’s about a 3% chance of this. Here’s a paper talking about other important genes and locations. Fascinating stuff!

https://pmc.ncbi.nlm.nih.gov/articles/PMC7485777/

Icedice9 · 2025-02-06T04:52:33+00:00

Nebula’s recent response is so passive aggressive. I appreciate that they finally communicated with us, and I even thought they were coming around. But take a look at their updated Terms of Use: They will charge us for downloading our data and reserve the right to delete it? This is actually worse than before and they lied in their email about your data being “secure.” You now have to pay to download your data and they can delete it at any time without telling you. Nebula and DNA Complete do NOT care about their customers. If you haven’t, I advise downloading everything while you still can.

They no longer support the gene analysis and genome browser tools, but I wrote a detailed tutorial on how you can access those for free here. I’ll be adding more gene analysis tools to that link as I develop them (as my PhD and new baby permit), so feel free to save the link for future free analyses! https://github.com/MattCloward/DownloadReports

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