[biocomputer]

Biocomputer: I'm using VM because a Windows PC is available and I don't know how to use bowtie in windows because I use it from command line. I have a question 1.5Gb is enough to run alignments?
Genomax: I use version 10.9.4 of OS X. Is it a problem?

Bowtie under windows is also run from the command line, cmd.exe. Or you can install Cygwin in Windows which will let you run the Windows version of Bowtie2 in Windows but using Linux style commands.

1.5GB is not enough for alignments, the Bowtie2 manuals says the human genome index needs 3.2GB so you'll probably need a computer with at least 4GB.

[ronton]

That is actually one of the nice things about Macs, they are bioinformatics software friendly. You can use Linux on a PC since Windows doesn't run a lot of the software, but with Mac OS can you can use the Bash shell, many scripts programs etc.

Skip the virtual machine. Use a computing core/cluster if you can, or your Mac, or a PC with Linux. Dual boot with Windows if need be rather than virtual machine. Just my 2c, I have seen a dramatic improvement running some of the same Java programs on 64-bit Ubuntu compared to 32-bit Windows 7, some just won't run and give errors.

[simobioinfo]

That is good. I was checking to see that you were not using an older version where you may run into problems.

Thank you Genomax! Now you encouraged me!

[GenoMax]

Genomax: I use version 10.9.4 of OS X. Is it a problem?

That is good. I was checking to see that you were not using an older version where you may run into problems.

[simobioinfo]

Biocomputer: I'm using VM because a Windows PC is available and I don't know how to use bowtie in windows because I use it from command line. I have a question 1.5Gb is enough to run alignments?
Genomax: I use version 10.9.4 of OS X. Is it a problem?

[GenoMax]

Starting with your Mac is certainly under your control.

Are you running a new(er) version of OS X (10.7.x or later)? Working natively in OS X would allow you to avoid the VM issue entirely.

[biocomputer]

I think your indexing is taking so long because with only 1.5GB allocated to the VM, bowtie2-build doesn't have near enough RAM so it is having to use a swapfile which will lead to thrashing and will make the process take a really, really long time. I just indexed the mouse genome mm10 for Bowtie2 using default settings and it used 5GB of RAM while building the index and took 4 hours on a large server, but even on a reasonably fast desktop computer as long as you have enough RAM it should be able to build overnight. I've indexed the mouse genome mm9 on an i7-2720QM in 6-8 hours. But anyways, as has already been mentioned you can download pre-built indexes. So you'll either have to download them or upgrade your RAM.

Also why are you using a VM? Bowtie2 is available for Linux, Windows, and Mac so you should be able to run it natively. With only 4GB of RAM you still won't have enough to build the index but when it comes to aligning then 4GB may be enough as long as you don't run many other processes at the same time.

[simobioinfo]

I would like to use institutional resources but I have been wait for a new PC for 2 years (in Italy research is very difficult) and now I have to start my work. So I think that using my Mac could be a faster and more reliable solution. Are you agree?

[GenoMax]

simobioinfo: I do not want to discourage you but if you are able to use institutional resources to do the actual computing you would find the experience much more enjoyable. You can certainly try and get started on the Mac and depending on your experience you may want to move to another resource using your Mac as the terminal to connect to that resource.

Note: Since you have a Mac you strictly do not need to use a VM. OS X is unix compatible and there are binary versions of tuxedo suite programs available that will natively run on OS X.

You can download pre-formatted indexes/annotations for human genome from the iGenomes site: http://support.illumina.com/sequenci...e/igenome.html This is a big download but hopefully you are using institutional network and would not have bandwidth issues.

[simobioinfo]

and do you think that expanding RAM is not the solution because VM is also a problem to run alignment?

[simobioinfo]

I have a Mac with 4GB of RAM and 1333Mhz. It is my personal machine but do you think I could use this computer to run analysis or Mac is not good?
Excuse me but I'm a newbie.

[simobioinfo]

Or I could allocate 3Gb of RAM for VM? It could improve indexing and other analyses?

[GenoMax]

Are you able to purchase more RAM? Please be aware that trying to do human data alignments in a VM is going to be a difficult task. You may be able to run a single alignment thread in the VM.

From Bowtie Manual

Bowtie 2 indexes the genome with an FM Index (based on the Burrows-Wheeler Transform or BWT) to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 gigabytes of RAM.

[simobioinfo]

Maybe I could expand RAM of my PC. What do you think about it?

[simobioinfo]

On my PC I have 4Gb of RAM. I suppose it could not be possible to allocate all 4Gb for VM. What can I do to improve performance of my PC?