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Genomics – A programmer’s guide

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Re: Genomics – A programmer’s guide

#31

Post by searine »

xyhopguy wrote: post #15
dannykwells wrote: post #14

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…

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.

>I was taught a decade ago that rolling your own in genomics isn't as bad of a decision as it seems.

Famous last words.

Re: Genomics – A programmer’s guide

#32

Post by astazangasta »

jghn wrote: post #13
magnamerc wrote: post #12

Earlier quoted context omitted.

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…

Actually about half of variation is private (not common) and commercial services will only look for common SNPs. So you will have some unique variants that would show up in a whole genome but not a SNP test.

Re: Genomics – A programmer’s guide

#33

Post by jghn »

astazangasta wrote: post #32
jghn wrote: post #13

Earlier quoted context omitted.

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…

Actually about half of variation is private (not common) and commercial services will only look for common SNPs. So you will have some unique variants that would show up in a whole genome but not a SNP test.

True. I was trying to say that your average lay person is unlikely to know the difference enough to be a big deal

Re: Genomics – A programmer’s guide

#35

Post by virtuabhi »

There are many people looking for introduction into genomics and NGS applications. One of the books I found to be extremely useful is Genomic Quirks (https://www.amazon.com/Genomic-Quirks-Search-Spelling-Errors...). This book explains genomic concepts with several case studies.

Here is a video by the author - https://www.youtube.com/watch?v=BfVo8EkeDVI

Re: Genomics – A programmer’s guide

#36

Post by la_barba »

zubyak wrote: post #28

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…

What sort of sequencing data are you planning to process? Are you planning to re-implement algorithms used by bwa/samtools or come up with something on your own? NGS is a very specialized field, so its very easy to get stuck in the weeds.

Re: Genomics – A programmer’s guide

#37

Post by aBioGuy »

This is a nice intro. For a good collection of "worked out" "pipelines" to analyze different kinds of genomic data types (RNA-seq, ChIP-seq) in the R environment (the concepts are universal, even if you don't R), take a look at Bioconductor:

https://www.bioconductor.org/packages/release/BiocViews.html...

Re: Genomics – A programmer’s guide

#38

Post by la_barba »

blopker wrote: post #11

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

I'm not an expert but AFAIK VCF isn't "raw" data. Raw data would be the output of a sequencer (fastq) which would be several gigabytes. I recently processed raw data from sequencing a tiny virus (~20k base pairs) and it was around 13GB. Human genome sequence data would probably be tens if not hundreds of GB.

Re: Genomics – A programmer’s guide

#39

Post by i000 »

la_barba wrote: post #38
blopker wrote: post #11

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

I'm not an expert but AFAIK VCF isn't "raw" data. Raw data would be the output of a sequencer (fastq) which would be several gigabytes. I recently processed raw data from sequencing a tiny virus (~20k base pairs) and it was around 13GB. Human genome sequence data would probably be tens if not hundreds of GB.

23andMe does genotyping not sequencing

Re: Genomics – A programmer’s guide

#40

Post by la_barba »

i000 wrote: post #39
la_barba wrote: post #38

Earlier quoted context omitted.

I'm not an expert but AFAIK VCF isn't "raw" data. Raw data would be the output of a sequencer (fastq) which would be several gigabytes. I recently processed raw data from sequencing a tiny virus (~20k base pairs) and it was around 13GB. Human genome sequence data would probably be tens if not hundreds of GB.

23andMe does genotyping not sequencing

Ah.. okay. I didn't know that. Yes that makes sense now that I think about it. They wont be able to do a full sequencing at their current price.
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