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-   -   computer specs for open-source tools (http://seqanswers.com/forums/showthread.php?t=62242)

cmccabe 08-25-2015 02:55 PM

computer specs for open-source tools
 
I am in the process of building a computer. My resources are limited but is an I5 with 16gb, 500gb sata hdd ok for tools like bowtie2, bedtools, picard, etc... I am planning to put 64-bit ubuntu 14.04.3 on it as well. Any thoughts/suggestions. Thank you :).

jwfoley 08-25-2015 06:48 PM

What kind of data will you be working with? Genomic DNA resequencing? RNA-seq for gene-expression profiling? RNA-seq for de novo transcriptome assembly?

16 GB memory will be a bit limiting. If you have RNA-seq data from a vertebrate and you want to use STAR, you'll need twice that much.

The i5 isn't anything to brag about either, but all that means is it might take longer to do things you're already not waiting for in real time anyway.

cmccabe 08-26-2015 03:48 AM

The data will be from genomic re sequencing of the medical exome(4500 genes). Thank you :).

GenoMax 08-26-2015 04:06 AM

If you have a certain budget then it is what it is. Maximize the memory/disk you can afford even if you need to step down a rung or two on the CPU speed/type. It will just take longer to get things done. Keep in mind that you will need to keep supplementing storage (offload data to external storage once analysis is done for a set) as you go along.

cmccabe 08-26-2015 04:26 AM

I guess I am just concerned that bowtie2 may not run. I guess as an alternative I could install it on windows 7 and use cygwin. Thank you :).

GenoMax 08-26-2015 04:53 AM

That would not be a good idea. Stick with straight linux unless you have a need for Windows on this machine for something else.

With 16G bowtie should run fine (human genome indexes need only ~3.2G of RAM, as you remember from a past discussion on this topic).

cmccabe 08-26-2015 04:58 AM

Thank you :).

GenoMax 08-26-2015 11:10 AM

Also on biostars: https://www.biostars.org/p/155793/


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