[winsettz]

Bowtie is through Galaxy, which I'm also in the process of trying to get my data uploaded on to.

I'm proposing that you deploy a linux vm, compile bowtie yourself and do it on your end. The alternative is Galaxy. Bioinformatics is a little challenging without either a powerful linux workstation to call your own, or the ability to use shared HPC machinery.

[KnowNothing2]

I'm proposing that you deploy a linux vm, compile bowtie yourself and do it on your end. The alternative is Galaxy. Bioinformatics is a little challenging without either a powerful linux workstation to call your own, or the ability to use shared HPC machinery.

Okay, so I downloaded ubuntu and bowtie. Now I'm completely lost on what I need to do.

[winsettz]

Okay, so I downloaded ubuntu and bowtie. Now I'm completely lost on what I need to do.

If you are interested in linux, this is a topic beyond seqanswers. For now, stick to galaxy to get your work done.

Is this for a class or a research project?

[KnowNothing2]

If you are interested in linux, this is a topic beyond seqanswers. For now, stick to galaxy to get your work done.

Is this for a class or a research project?

I'm actually a PhD student. Unfortunately, I have very little knowledge on computer science and bioinformatics. I will seek professional assistance, but I wanted to give it a shot myself.

[KnowNothing2]

Using Galaxy, I have converted my fastq file to illumina 1.3-1.7 using FastGroomer. Now I am trying to align it using Bowtie, but it is just sitting in queue (has been for an hour). Am I doing something wrong?

[SNPsaurus]

Sounds like the typical public Galaxy experience. For something intensive like alignment, it could take overnight.

[Markiyan]

Time to get your's own "cloud" under the bench.

It may be a bit off topic, but if I would have to start from scratch...

Okay, so I downloaded ubuntu and bowtie. Now I'm completely lost on what I need to do.

1. Sort out your's workspace. (ideally with admin/linux mate)
Ideally you want get access to a linux system (ask uni sys admins) or find a linux-friendly mate, and tell him, that you want a high-end linux64 bit system.
(If he is a gamer - tell him you want something that you can play Chrysis on, but with cheap videocard and several 2-4TB drives).

So now you need to install ubuntu 64 bit (or fedora or other 64bit linux) on yours box with at least 8GB of ram (ideally get 32-64GB in). Have a dedicated box for it or at least put a new empty HDD into it first (so you don't wipe yours windows/data), disable secure boot (if enabled) and have a go. Don't be afraid to experiment with empty drives, (disconnect any data ones during install).

If you have problems/trouble doing it(installing ubuntu/fedora/mint) - you can try booting into knoppix into 64 bit mode:
a. Insert knoppix DVD/USB and boot from it.
b. on the prompt type:
knoppix64 dma 3
c. once booted and having a prompt do the following:
cd /media
ls
mount sda1
mount sdb1
(...and so on - for each entry from ls). -> if any problems mounting NTFS - than boot into:knoppix dma, and press [Ctrl]+[Alt]+[F2] to get to the root console...
(once data partition is mounted do
mc
(Starts Midnight Commander (similar to Far manager for windows/Norton for DOS) - see google how to use them - use arrows+enter+tab for navigation, F5 for copy, F4 for edit...).

One of sd* should be the location with your's data/bowtie

d. extract/compile bowtie:
tar -xf [Bowtie_sourtce].tar.gz
cd [Bowtie_sourtce_dir]
./configure
make

2. Try doing data processing. Try small/test dataset first...
e. copy bowitie to the fastq files location (or to /bin) and try running it...

...
Make sure to keep your's data in the /media/sd* subfolders, or it will be lost once power down/reboot...
...
To shut down do:
halt
and wait for PC to switch off.

PS: Have an internet connected device to hand, and use it for googling any answers while setting up your's main workspace...
Good luck.

Also when dealing with cloud use your's uni WIRED network, ADSL suc*s for upload speeds...