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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
You may (at your own risk) take a look at
Unfortunately, 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…
Which phenomena are you referring to exactly? That we have two copies of each chromosome and if they mean we have two copies of the human genome?
> Are there two copies of the XY chromosome, too?
Each of our non-sex cells[1] contain two sex chromosomes: one from our father and one from our mother. Since your mother always inherits her X chromosome, your sex is determined by which sex chromosome you got from your father. If you are a female (XX), your father passed on his X chromosome. If you are a male (XY), your father passed on his Y chromosome.
This rule makes for some interesting inferences. For example, your father in turn got his X chromosome from your grandmother and his Y chromosome from your grandfather (both on your father side, of course). Your mother, on the other hand, got his X chromsome from both your grandparents on her side.
So if you're a male, your Y chromosome was passed on from your grandfather on your father's side. If you're a female, one of your X chromosome comes from your grandmother on father's side, but your other X chromosome may come from either of your grandparents on your mother's side.
You can trace this Y-chromosome lineage back to what's called the Y-Chromosomal Adam, which is the last universal common ancestor of all currently living human males[2]. You can make a similar inference using your mitochondrial genome[3] and arrive at what we call the Mitochondrial Eve[4].
Our sex cells[5] are different, since they only have one copy of our chromosome set. The number of the chromosome set we have is called ploidy[6] and so our sex cells are haploid cells, as opposed to our non-sex cells, which are called diploid.
If you're a male, a single mature sperm cell in your body contains either the X or Y chromosome. For females it's different, since they only have the X chromosome, all their mature cells contain only one copy of the X chromosome.
[1] https://en.wikipedia.org/wiki/Somatic_cell
[2] https://en.wikipedia.org/wiki/Y-chromosomal_Adam
[3] https://en.wikipedia.org/wiki/Mitochondrial_DNA
[4] https://en.wikipedia.org/wiki/Mitochondrial_Eve
CoFest is a collaborative two-day working session. The only requirement for attendance is that you have an interest in open source software and solving scientific problems. We will have contributors to open source bioinformatics tools present to collaborate with, and we welcome new attendees who want to learn and contribute to open source code, documentation, workflows, or training.
This year CoFest is July 26-27 in Basel, Switzerland. There is no registration fee to attend in person or virtually.
Disclosure: I'm on the organizing committee for BOSC and CollaborationFest
Unfortunately, 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…
The red chunks are its DNA. But they're 'chunky' because the 'whole genome' is partitioned into 23 chunk - each chunk is a 'chromosome'. And each chromosome comes as a pair. And in the movie you can see the cell split the pairs, where one set goes to one cell, and the other set goes to the other.
If you notice, in the cells just prior to 'condensing', the nuclei (red stuff) looks kind of brain-like in its topology. Those are the chromosomes as well, just relaxed and spread out.
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
For academic use, UK Biobank, 1000 Genomes and other resources offer variants for large groups, my wife included. You may (at your own risk) take a look at https://opensnp.org/
Unfortunately, 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…
Animals tend to have the same number of chromosomes at all times, and they tend to come in pairs that are nearly identical. There are various ways of mapping chromosomes that yield unique fingerprints that are stable under the level of variation we typically see in a species (see restriction mapping for example), so we can take a particular fingerprint and call it chromosome 1 or 2 or whatever. Animals have two copies of chromosome 1 and two copies of chromosome 2, etc. There are individuals who don't, who have a single copy of one or extra copies, and this causes problems, such as Turner syndrome. Similarly, when animals reproduce, each parent produces a germ cell (sperm or egg) that has one of each of the chromosome pairs. One of the reasons that many hybrids like mules are sterile or nearly infertile is that their chromosomes, coming from different species, aren't in pairs, so when they pass on half of them, there may be necessary hunks of DNA that just aren't passed on.
Other species have different numbers of copies of chromosomes, and may vary. Depending on point in lifecycle and conditions, some plants range from two copies to hundreds. Dinoflagellates tend to have four for interesting reasons that I believe are related to the Byzantine generals problem.
There is no XY chromosome. Females in mammals follow the normal pattern with the X chromosome: they have two of them and they are passed on like any other chromosome. Males are weird. They have one copy of X and a copy of a shrunken chromosome called Y. Note that this is only mammals. Birds and reptiles have a totally different set of chromosomes for sex determination, and in some vertebrate orders the chromosomes don't fully determine sex. Incubation temperature often changes it.
I'm a cs student, in my thesys I'll be working on a NGS C++ application. I need at least a brief introduction to "basic" sequencing but I'm struggling to find something accessible. Every book I find seems superspecialized. Now I'm reading "Insect Molecular Genetics : An introduction to principles and applications" but I'd like to read just a book chapter a little bit more advanced than the contents shown in this video https://youtu.be/ONGdehkB8jU
Any suggestions?
The 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…
My experience has been translating domain data into spark has a 100X improvement in data analysis.
Maybe it's off topic, but anyway : I'm a cs student, in my thesys I'll be working on a NGS C++ application. I need at least a brief introduction to "basic" sequencing but I'm struggling to find something accessible. Every book I find seems superspecialized. Now I'm reading "Insect Molecular Genetics : An introduction to principles and applications" but I'd like to read just a book chapter a little bit more advanced t…
On the other hand, as a person who’s worked on sequencing software I’ve found the biochemistry knowledge to only be incidentally useful - though I may be underestimating some of the “basic” assumptions that were used day to day.