SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
mosaik-aligner installation problem on redhat 6 joachim.jacob Bioinformatics 5 05-10-2013 08:36 AM
RNA-Seq: A Powerful and Flexible Approach to the Analysis of RNA Sequence Count Data. Newsbot! Literature Watch 0 08-04-2011 02:00 AM
Ion Torrent PGM data with Mosaik-aligner Magnus Bioinformatics 0 05-19-2011 03:59 AM
Mosaik-aligner for SNP detection, Need Help. ketan_bnf Bioinformatics 2 12-22-2010 09:17 PM
Mosaik Aligner problem with SOLiD sequences g_solid Bioinformatics 0 02-07-2010 05:30 PM

Reply
 
Thread Tools
Old 02-02-2010, 03:39 AM   #1
neni
Junior Member
 
Location: CH

Join Date: Feb 2010
Posts: 3
Question Powerful PC for MOSAIK aligner?

For mapping 454 reads against human genome with MOSAIK, which configuration would you recommend?
PC with
a) two quad core 2.26GHz processors and 24GB RAM or
b) two quad core 2.40GHz processors and 12GB RAM

in other words, whats more important: the processor or RAM capacity?
neni is offline   Reply With Quote
Old 02-02-2010, 12:04 PM   #2
mkeehan
Member
 
Location: Hamilton NZ

Join Date: Feb 2010
Posts: 13
Default

My jump database was about 20 GB in size. Having that all in memory is much faster than swapping to disk. So I'd go for the large memory but it really depends on the size of the jump database you will use.
mkeehan is offline   Reply With Quote
Old 02-03-2010, 06:35 AM   #3
drio
Senior Member
 
Location: 4117'49"N / 24'42"E

Join Date: Oct 2008
Posts: 323
Default

Quote:
Originally Posted by neni View Post
For mapping 454 reads against human genome with MOSAIK, which configuration would you recommend?
PC with
a) two quad core 2.26GHz processors and 24GB RAM or
b) two quad core 2.40GHz processors and 12GB RAM

in other words, whats more important: the processor or RAM capacity?
This may help you:

http://seqanswers.com/forums/showthread.php?t=2566
__________________
-drd
drio is offline   Reply With Quote
Old 04-30-2010, 02:13 AM   #4
Gianza
Junior Member
 
Location: Italy

Join Date: Jan 2010
Posts: 7
Default

Hello everybody,
I'm struggling with the same problem.
I'm on the way to buy a desktop/workstation.
My project is the following- eukaryote-plant
-454 EST assembly 1,5 M reads from 3 different samples (for SNP mining)
Looking to use MIRA, the extimated memory usage is 8 Gb. OK
-Solexa reads (always from cDNA) mapping to reference sequence (generated
by 454) ; aprox. 30 M reads to map (always for SNP mining on other
samples).For this one I'm looking to use MOSAIK (MIRA gave me an exitation
of memory around 30 Gb).

The question is the following:
Does a desktop/workstation with a quad-core (intel i7 860) with 12 Gb can handle this kind of Solexa mapping, or, any scripts will run out of memory??
I'm also considering to install 24 Gb instead of 12 Gb but I cannot understand if this might be crucial or just wasted money (because there is no way to run a Solexa mapping without a powerful cluster).
I mean, I don't care if the assembly will take one or two days; but I just wanna make sure it will be accomplished without crashing. In other word, having a cluster with 256 Gb of RAM, is just a matter of run time or it is the pivotal point to avoid the assembler to crash?

Can anyone give me some highlight on what I should expect from such a machine I'm planning to buy.

Thanks, I will appriciate.

Davide
Gianza is offline   Reply With Quote
Old 04-30-2010, 02:45 AM   #5
ymc
Senior Member
 
Location: Hong Kong

Join Date: Mar 2010
Posts: 498
Default

Quote:
Originally Posted by Gianza View Post
Hello everybody,
I'm struggling with the same problem.
I'm on the way to buy a desktop/workstation.
My project is the following- eukaryote-plant
-454 EST assembly 1,5 M reads from 3 different samples (for SNP mining)
Looking to use MIRA, the extimated memory usage is 8 Gb. OK
-Solexa reads (always from cDNA) mapping to reference sequence (generated
by 454) ; aprox. 30 M reads to map (always for SNP mining on other
samples).For this one I'm looking to use MOSAIK (MIRA gave me an exitation
of memory around 30 Gb).

The question is the following:
Does a desktop/workstation with a quad-core (intel i7 860) with 12 Gb can handle this kind of Solexa mapping, or, any scripts will run out of memory??
I'm also considering to install 24 Gb instead of 12 Gb but I cannot understand if this might be crucial or just wasted money (because there is no way to run a Solexa mapping without a powerful cluster).
I mean, I don't care if the assembly will take one or two days; but I just wanna make sure it will be accomplished without crashing. In other word, having a cluster with 256 Gb of RAM, is just a matter of run time or it is the pivotal point to avoid the assembler to crash?

Can anyone give me some highlight on what I should expect from such a machine I'm planning to buy.

Thanks, I will appriciate.

Davide
You can also buy two 15K RPM SAS drives or two WD 10K SATA drives to form RAID0 for the swap memory. You can try this before you spend big money on the RAM.
ymc 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 03:13 AM.


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