If anyone is interested in playing with a full 23andMe raw data file (VCF), I have mine on GitHub: https://github.com/blopker/DNA PRs welcome!
If you're also interested in working on this stuff, shoot me an email ;) blopker@23andme.com
Genomics – A programmer’s guide
11–20 of 53 posts
Re: Genomics – A programmer’s guide
#12If anyone is interested in playing with a full 23andMe raw data file (VCF), I have mine on GitHub: https://github.com/blopker/DNA PRs welcome! If you're also interested in working on this stuff, shoot me an email ;) blopker@23andme.com
How far are companies like 23andMe from entire genome sequencing? That's kind of what I'm waiting for. Can you still get valuable data from genotyping?
Re: Genomics – A programmer’s guide
#13If anyone is interested in playing with a full 23andMe raw data file (VCF), I have mine on GitHub: https://github.com/blopker/DNA PRs welcome! If you're also interested in working on this stuff, shoot me an email ;) blopker@23andme.com
How far are companies like 23andMe from entire genome sequencing? That's kind of what I'm waiting for. Can you still get valuable data from genotyping?
You can get valuable data from genotyping. SNPs contain the bulk of variation between you & me.
For your first question it depends on your definition of "companies like 23andMe". There are numerous companies that'll do a whole genome for you, but I don't know if any of them do the writeup about it that 23andMe provides. 23andMe did at one time offer an exome product, but stopped that a while back.
The largest hurdle is cost. Whole genomes, even exomes, are significantly more expensive than a SNP chip. As most would be users don't know enough to care it doesn't make much economic sense to offer those to the masses at the moment.
Re: Genomics – A programmer’s guide
#14The hardest part of genomics for me has honestly been figuring out which open source poorly maintained tool I should use for a particular problem. and which options should be run and how the data need to be preprocessed before hand.
I mean has anyone ever actually read the documentation of the GATK? It is famously dreadful. And that's professionally maintained.
Honestly a nice addition here would be a "so you want to" with snippets of raw FASTQ or VCF data and working code for various operations, maybe with an accompanying Docker container.
Re: Genomics – A programmer’s guide
#15The hardest part of genomics for me has honestly been figuring out which open source poorly maintained tool I should use for a particular problem. and which options should be run and how the data need to be preprocessed before hand. I mean has anyone ever actually read the documentation of the GATK? It is famously dreadful. And that's professionally maintained. Honestly a nice addition here would be a "so you want to…
have you ever looked at the test suites for Picard? All regression tests and the library is OO hell lols
I was taught a decade ago that rolling your own in genomics isn't as bad of a decision as it seems.
Re: Genomics – A programmer’s guide
#16Unfortunately, the article handwaves the one thing I’ve been struggling with the most: chromosomes.
What is the relationship between chromosomes and the human genome?
I somewhat get that a chromosome is somewhat of a partition of the genome, but how does the „two copies“ phenomenon of the human genome and the „two copies“ thing of chromosomes fit together? Are those one and the same concept?
Are there two copies of the XY chromosome, too?
Re: Genomics – A programmer’s guide
#17If anyone is interested in playing with a full 23andMe raw data file (VCF), I have mine on GitHub: https://github.com/blopker/DNA PRs welcome! If you're also interested in working on this stuff, shoot me an email ;) blopker@23andme.com
I hope you got all of your kids and relatives to sign off on that, if you have any.
Re: Genomics – A programmer’s guide
#18“Wall Street trader to Australian Aboriginal”
Can’t someone be both?
Re: Genomics – A programmer’s guide
#19Unfortunately, the article handwaves the one thing I’ve been struggling with the most: chromosomes. What is the relationship between chromosomes and the human genome? I somewhat get that a chromosome is somewhat of a partition of the genome, but how does the „two copies“ phenomenon of the human genome and the „two copies“ thing of chromosomes fit together? Are those one and the same concept? Are there two copies of t…
You have 46 chromosomes. Each chromosome is one massive contiguous molecule of DNA, which can be represented as a string of (up to) 150 million letters ("nucleotides") drawn from {A, C, G, T}. Together, the whole human genome is roughly 3 billion nucleotides. Since you have two copies in each cell, you have 6 billion nucleotides in total.
Each chromosome is either an autosome or sex chromosome. The autosomes are chr1 to chr22. All people (excepting those with chromosomal disorders, like trisomy 21) have two copies of each autosome, with one copy coming from each parent. Then, for the sex chromosomes:
* If you're male, you get an X chromosome from your mom and a Y chromosome from your dad.
* If you're female, you get an X chromosome from your mom and another X chromosome from your dad.
So, yes, "two copies of each chromosome" and "two copies of the genome" are the same concept, since the genome consists of chromosomes.
Re: Genomics – A programmer’s guide
#20Genetics is an extremely fun topic but the learning curve for entry has been non-trivial. It reminds me of the struggles I had when I was first learning to program recursive functions. With that said, it's been far, far more complicated than recursion. So, thank you for the resource, I'm always happy to find content sources that are helpful on the subject. If you enjoy hard CS problems, bioinformatics has been booming and I don't really see it slowing down anytime soon.
As for some resources, these books have been the most helpful for me.
[0] https://www.amazon.com/Molecular-Biology-Cell-Bruce-Alberts-... // I've linked and have seen mentioned here in the past, a great intro to cell biology.
[1] https://www.amazon.com/System-Modeling-Cellular-Biology-Conc... // Modeling with math. I would consider this high-yield as it gave me a great deal of insight into what different code bases are actually attempting to do.
[2] https://www.amazon.com/DNA-Nanoscience-Prebiotic-Emerging-Na... // Blew my mind when I first read it but the content is pretty standard as far as genetics course material goes.