How to set up a new GEO project

You can use geofetch to quickly set up a project to run with looper.

Download data

geofetch -i GSE69993 --just-metadata -m metadata

Initialize looper

Make it easier to run looper without specifying the config

looper init metadata/*.yaml

Convert to fastq

Now, you can convert the files from sra into fastq format:

looper run --amend sra_convert

Run pipeline

Add a pipeline interface to link to a project


looper mod "pipeline_interfaces: /path/to/piface.yaml"