Minimum requirements for a laptop to do rna seq analysis
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3 months ago
ashaneev07 ▴ 20

Hi everyone

I have few years of break from my career as a bioinformatician. So to upgrade myself is much needed since I'm looking for a laptop to perform some RNA-seq, ChIP-seq analysis (not bulk data analysis) what would be the minimum specification required?

Thank you

chip-seq rna-seq ngs • 880 views
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ssh

Joking aside, it depends how big the datasets are - are you planning on it being human data?

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Of course not human data. I just want to familiarize some pipelines regarding rna seq/chip seq analysis with minimum data. Wants to know how it works..

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This is going to be limited by your budget. How much money can you toss at this laptop?

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Between 30k -50k. I don't want to run an entire set of data for analysis. I just want to run some pipelines related with rna seq, chip seq, etc to know how it works. But there is a minimum hardware requirements for these kind of analysis.

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You'll primarily be RAM limited probably, so get as much as you can.

Any laptop from a decent name brand in the £1,500-£2,000 bracket should be pretty much fine. If you have the option to configure the spec, then just optimise for more RAM. I'd expect a computer these days to come with a minimum of 1TB of solid state storage and 8-16 CPU cores/threads. I would basically ignore the GPU specs unless you intend to use GPU acceleration (still quite rare in bioinformatics) or aim to do a lot of ML in future.

If you go apple, just bear in mind that Apple silicon is not as widely supported in the bioinformatics community still.

Almost any spec can manage run these analyses, albeit suboptimally, so you could spend less, but they will just be slower. RAM will be the main hard limit making something completely insurmountable though.

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30,000-50,000 units of which currency?

Joe 's suggestion here is probably the best way forward: most CPUs have at least 4 cores now, so this is not really a deciding factor; instead get a machine with as much RAM as possible. Or at least get one that can accept a lot of RAM and upgrade it as the need arises -- most business laptops like the HP Elitebooks (or the much more affordable but otherwise equivalent Probooks) will have two RAM slots that can support a total of 64GB (or at least 32GB) of memory. It might be worth getting a machine that supports DDR5 but DDR4 memory appears to be quite inexpensive right now so you might want to go for that if you want to max out the RAM right from the get go.

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30,000-50,000 units of which currency?

Based on OP profile INR (indian rupee). About USD 400-600.

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Unless its going to be second hand then or something, a $500 laptop is going to be pretty basic

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If this is the case, then a used Elitebook (G7, G8, or if lucky, G9) is probably the best way forward.

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