How to run BAGEP in conda environment? about bagep HOT 3 CLOSED

Hi,

Apologies, I am just seeing this as I did not get a notification earlier.

Your paired-end FASTQ files can be in the same directory you cloned from github or you can simply structure it in a new directory named fastq

To run the pipeline, just type snakemake --config ref={ref_genome}

What {users reference genome} indicates is the path to where your reference genome is stored, it can be in the data/ directory

For example: snakemake --config ref=./data/kleb.fna --cores 4

from bagep.

Thank you @idolawoye for your response.
I'll let you know if this works.

from bagep.

I am closing this issue now that it has been 15 days since your response, Let me know if there is anything I can help with

from bagep.