A Basic Tutorial on Analyzing the Coronavirus Genome

I suspect not, sorry. I can send you the files needed to view the data in IGV over email though.

It seems you have become desensitized to the pain

You’re not wrong. :slight_smile:

My current PC would buckle on the computing load for complex genomes or possibly even this SARS-CoV-2 variant analysis. She is an old head and in dire need of replacement. I suspect you don’t use a laptop for your regular type of analysis?

Nope, I do almost all of my work on a lab server or on my university’s computer cluster. This example analysis probably could be done on a laptop in a pinch, but scaling up to organisms with larger genomes would likely be challenging.

Yeah, but I suspect they would be more computationally intensive to analyze relative to normal human cells. I saw a scary karyogram of some tumor cells: some chromosomes had four copies, others three. Variant analysis of those cells should require more than the usual.

Interestingly, variant analysis of non-haploid samples still relies on a haploid genome, so the computational burden might not be too different (although it might still be higher). Duplicated segments (including whole chromosome duplications) would show up as regions of highly elevated read depth compared to the rest of the genome.

The trick is to install “Docker” and spin up a Linux OS in the Docker container. You’ll have to learn a bit about the command line.

Cygwin is helpful as starting point from which to launch docker containers on Windows.

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Since I started down a similar path a few months ago I thought I would share a bit from my experience.

Cc: @Michael_Okoko

I’m using a pretty fast desktop PC to analyze Illumina reads of viral transcripts and I can push through 20 million 150 bp reads in just a few minutes. A slow laptop should get the job done. Small genomes drastically reduce compute times, in my very limited experience.

I started using Linux for the first time just a few months ago and I have stumbled my way through. What really helped me was to use a text editor to create lists of file and script locations so I could copy and paste them into command lines that I also wrote within the text editor.

I had a student install a Windows/Linux dual boot and that works great, but is a bit inconvenient for jumping between Linux and Windows programs. I can’t speak to the Docker container, but if @swamidass thinks it will work then I would follow his advice. I might even look into it for my own work.

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Just curious. You can plot a phylogeny from the sequence reads, right? Can you also check to see if the South African or UK variants are amongst the Mexican samples?

Technically you could, but you really shouldn’t. Due to the immense amount of redundancy and the presence errors in the reads, it’s much more practical to either assemble the reads and build a tree from the assembled sequence or use the reads to call variants and infer the haplotype of each sample and build a tree from the haplotypes and/or variants.

Can you also check to see if the South African or UK variants are amongst the Mexican samples?

I believe these samples were collected several months before the SA or UK variants were identified, so they are likely not present.

You might be surprised :smile:

That’s true, I might be.

Also, sorry for neglecting this thread. I’ve been swamped. I’ll get back to it as soon as I can.

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Weird. I looked at it but no clue why it does that. Maybe I will ask on Discourse.Meta

I have an answer:

I don’t really understand the answer, but there it is. something to do with format highlighting which is useful on coding forums.

An easier solution os to remove the extra backquotes (`). I don’t understand why that works either.

@swamidass I posted a question to Discourse.Meta about this green text, and they gave a solution you might want to see. I think this is a minor problem tho, and we occasionally have people posting code, so I recommend just leaving it alone.

@davecarlson can fix it himself by adding “text”. I’ll look into changing the forum settings.

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I saw that I was “summoned” though the response seems to have been deleted. Thanks for the reminder. Things are kind of crazy at the moment, but I promise to return to this as soon as I can!

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