Posted by yreg 4 days ago
Also gotta shout out to these incredible molecular animations by WEHI: https://www.youtube.com/watch?v=7Hk9jct2ozY
For example, sequencing instruments include base quality strings in the output. Base qualities are estimates how likely the instrument got each sequenced base right. But most people don't want to store that much noise, especially when the actual data is highly compressible. So the base qualities get quantized using more or less principled methods that seem to work well empirically.
Read aligners make similar estimates of how likely they got the correct alignment for each read. Those estimates are typically based on simplistic models and a number of assumptions. There are two main components in the estimate. One is based on comparing the primary alignment the aligner chose to the secondary alignments it also found. Another is an estimate that the aligner didn't find the correct alignment, because that part of the sequenced genome is too different from the reference. The latter is obviously handwavy. And the aligner cheats in the former. Because people don't want to wait 10x or 100x longer for better results, the aligner gives up early and estimates how good secondary alignments it might have found if it had actually done the work.
And then there is variant calling. At some point, the state-of-the-art callers were statistical. But then people got better results with neural networks. Or at least the results were empirically better.
But they produce short reads, and because DNA is full of repetitive fragments, it's not always clear where the read came from.
We also have two copies of genes, which also further complicates matters.
The first startup where I worked, developed synthetic long reads on top of Illumina's hardware. We could stitch together 50kbp reads, which really helped with de-novo sequencing.
I'd strongly recommend in reading up on the parts of cell biology that come after this. Otherwise you'll get the wrong impression of how messy biology actually is.
There's the X and Y chromosomes, those produce a binary result (unless you have a genetic anomaly). And after that comes the messy and fuzzy parts I mentioned, where those genes trigger changes in hormone levels and development. And those parts are analog, very complex and contain a lot of different parts. So the outcome is not binary anymore.
There are more combinations than merely having only X, or an XY combination. And there is more fuzziness even in the Y and X expression, as you said. It's fuzzy all the way down. The tale of Binary results has always been from compression of reality: Always has been.
But you're right, the full range of biological possibilities is very fuzzy . SRY itself a just a regulatory switch that other sex-linked traits are conditionally dependent on. If the switch gets broken, you develop as female. If genes that support the switch break, you might develop as female. If a sex-linked trait downstream from SRY mutates, then pretty much anything can happen. And other species do sex determination completely differently. Hell, a lot of bacterial sex basically involves throwing pseudo-viruses at each other.
It's definitely possible to learn enough to be productive within a few months, but to actually comprehend and understand the underlying biology takes much, much longer. I still don't understand much of what is presented by people from other labs outside of my specialty.
Maybe a section on RNA degredation and DNA stability and how it would affect sequencing would be nice.
Also, down stream analyses are largely missing e.g. differential analysis, pathway enrichment. Not to mention newer single cell techniques and their up/down sides. But good start!