Buy PC for Exome sequencing
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6.5 years ago

Hi!

Im new at this forum and just started 2-3 weeks ago to learn bioinformatic, I'm biology.

First thanks to all for all he tutorials has provide for people like me to introduce themselfs in this interesting world :) even many times I crash my head and get desperate.

My source are fastq and bam files around 20-26 gb, which generate me lot headaches when I work with a 3gb ram old dell laptop....At the moment I get stock at alignment because ou of memory, when i get the unmmaped sequence to retrive possible viral load..I can work only with the 20 gb file if i use the 26gb i get "core dumped" ;_; So I have decide to buy a stationary pc.

I cant spend so much money atm so I need something usefull and cheap, I thought about AMD FM 8350 8x, a cheap mainboard like Asrock 980DE3/U3S3 and 32 gb ram. Would be this enough? or I must go for intel?

I use mainly Linux.

Whatever advice will be welcome! :))) Thanks!

sorry for my bad grammatic (spanish lady)

sequence alignment genome • 1.5k views
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AMD/Intel does not matter as long as your favorite linux distro works. If you can only fit in 32G in your budget that should be fine. Unless you play games on your PC don't invest in a fancy graphics card. Use that money towards an SSD for your system disk (256G should be enough). Get larger regular disk(s) for your data.
Having said that I recommend that you try to find centralized IT resources at your institution/organization for this kind of work. That way you can use any computer/terminal to access those resources and not have to invest in local hardware.

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Before you buy something yourself, see if there is a computer resource available to you. In particular, is there a shared compute system that you could access? Informatics is not just about "running jobs" but also about software installation, data integrity, network, etc.

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6.5 years ago

You could also try using Galaxy and their servers for these standard tasks.

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6.5 years ago
igor 13k

You can try Illumina BaseSpace to the analysis for free. For standard analysis, it should be sufficient.

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6.5 years ago

thanks a lot for the information!!!

Atm I do this as a hobby and hope in september I will be able to do a master in bioinformatic :)

Best regards!

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