[Sow]

could not locate bowtie index corresponding to biobase "e_coli"

Hi,

I am trying to use bowtie from my environmental variable-
$ Module load bio/bowtie/1.1.2
$ bowtie e_coli reads/e_coli_1000.fq
But it returns me the following:
Could not locate a Bowtie index corresponding to basename "e_coli"
Command: bowtie --wrapper basic-0 e_coli reads/e_coli_1000.fq

I thought e_coli indices comes with the package - so this this should be a easy command to run.
Could someone guide me about what is the right command?

[dpryan]

Environment modules only put the executable in the PATH, nothing more. You'll still need to tell bowtie where the indices are (assuming they were even installed).

[Sow]

Thank you so much! I had to specify my home directory for the genome and the read file.