Running bowtie on Ubuntu

[KnowNothing2]

So I installed bowtie on ubuntu. I'm following the "getting started" instructions (http://bowtie-bio.sourceforge.net/tutorial.shtml) from bowtie, so I typed the following into the terminal:

bowtie e_coli reads/e_coli_1000.fq

Obviously, this didn't work because the path is wrong, but when I get into the correct directory and try to run "e_coli_1000.fq" using the command "./e_coli_1000.fq", it spits out all kinds of syntax errors.

Anyone know what may be the problem?

[JackieBadger]

if you do not put the bowtie binary in your PATH variable you must go to the directory which contains the binary file and use

./bowtie path/to/input/file.fq -options

Also, use bowtie2

[KnowNothing2]

if you do not put the bowtie binary in your PATH variable you must go to the directory which contains the binary file and use

./bowtie path/to/input/file.fq -options

Also, use bowtie2

I was going to use bowtie2, but it looks like only bowtie has a practice dataset to learn the system

I don't know much about terminal, I'm trying to learn at the moment. So I'm not quite familiar with PATH variables and the sort.

[JackieBadger]

http://bowtie-bio.sourceforge.net/bo...-phage-example