Bowtie2 index error help - beginner

[archaeogen]

Hi guys,

I am a newbie to bioinformatics and having some trouble getting a grip on a Bowtie2 index.

I have my 2 files (wu_0_A_wgs.fastq and wu_0.v7.fas) located in /home/guest

when I run the following command.

bowtie2 -p 4 -x /home/guest/wu_0 wu_0_A_wgs.fastq -S wu.bt2.sam

I get the following error:
Could not locate a Bowtie index corresponding to basename "/home/guest/wu_0"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /usr/local/bin/bowtie2-align-s --wrapper basic-0 -p 4 -x /home/guest/wu_0 -S wu.bt2.sam wu_0_A_wgs.fastq
(ERR): bowtie2-align exited with value 1

I am trying to see how my input is not allowing the index to take place.
The help shows an input:
bowtie2 [options]* -x <bt2-idx> {-1 <m1> -2 <m2> | -U <r>} [-S <sam>]
Just can't see where i'm going wrong.
Any advice would be amazing!
Thank you

[GenoMax]

Is "wu_0.v7.fas" the reference fasta file and the other file actual reads?

You would need to create an index separately with the reference fasta first. Something like

$ bowtie2-build wu_0.v7.fas wu_indx

This will create multiple files with "wu_indx" name as prefix. These files constitute the bowtie index.

You will then align your fastq file against this reference genome index:

$ bowtie2 -p 4 -x wu_indx -U /home/guest/wu_0_A_wgs.fastq -S wu_aligned.sam

[archaeogen]

Thanks for your help...
yes wu_0.v7.fas is the reference fasta.

Running that exact code:
$ bowtie2 -p 4 -x wu_indx -U /home/guest/wu_0 wu_0_A_wgs.fastq -S wu.bt2.sam I get the following error:

Extra parameter(s) specified: "wu_0_A_wgs.fastq"
Error: Encountered internal Bowtie 2 exception (#1)
Command: /usr/local/bin/bowtie2-align-s --wrapper basic-0 -p 4 -x wu_indx -S wu.bt2.sam -U /home/guest/wu_0 wu_0_A_wgs.fastq
(ERR): bowtie2-align exited with value 1

Quite confused as to why..
Thanks again

[GenoMax]

Sorry. My mistake. I had copied and pasted your original command and forgot to take out two extra words that were there. Corrected version is in post #2. Please try that.

[archaeogen]

Thank you heaps for your help!