SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Open source tools for 23andMe data adaptivegenome Bioinformatics 6 02-10-2016 07:45 AM
Open source bioinformatics tools: Blaster, Primer Factory, Labtools snowformatics Bioinformatics 0 01-20-2015 05:45 AM
Open source tools for whole genome analysis. man4ish Bioinformatics 1 04-22-2014 05:11 AM
Computer specs for RNA-seq S.pombe Parharn Bioinformatics 8 01-24-2014 06:06 AM
Bioinformatics Computer: List your specs peromhc Bioinformatics 14 10-09-2009 10:21 AM

Reply
 
Thread Tools
Old 08-25-2015, 02:55 PM   #1
cmccabe
Senior Member
 
Location: chicago

Join Date: Jul 2012
Posts: 354
Default 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 .

Last edited by cmccabe; 08-25-2015 at 03:34 PM.
cmccabe is offline   Reply With Quote
Old 08-25-2015, 06:48 PM   #2
jwfoley
Senior Member
 
Location: Stanford

Join Date: Jun 2009
Posts: 181
Default

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.
jwfoley is offline   Reply With Quote
Old 08-26-2015, 03:48 AM   #3
cmccabe
Senior Member
 
Location: chicago

Join Date: Jul 2012
Posts: 354
Default

The data will be from genomic re sequencing of the medical exome(4500 genes). Thank you .
cmccabe is offline   Reply With Quote
Old 08-26-2015, 04:06 AM   #4
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,053
Default

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.
GenoMax is offline   Reply With Quote
Old 08-26-2015, 04:26 AM   #5
cmccabe
Senior Member
 
Location: chicago

Join Date: Jul 2012
Posts: 354
Default

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 .
cmccabe is offline   Reply With Quote
Old 08-26-2015, 04:53 AM   #6
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,053
Default

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).
GenoMax is offline   Reply With Quote
Old 08-26-2015, 04:58 AM   #7
cmccabe
Senior Member
 
Location: chicago

Join Date: Jul 2012
Posts: 354
Default

Thank you .
cmccabe is offline   Reply With Quote
Old 08-26-2015, 11:10 AM   #8
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,053
Default

Also on biostars: https://www.biostars.org/p/155793/
GenoMax is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:58 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO