tutorial

Prerequisites

You must have the sratoolkit from NCBI installed, with tools in your PATH (check to make sure you can run prefetch). Make sure it's configured to store sra files where you want them. For more information, see how to change sratools download location.

Download SRA data using geofetch

To see full options, see the help menu with:

geofetch -h

For example, run it like:

geofetch -i GSE##### -m path/to/metadata/folder -n PROJECT_NAME

This will do 3 things:

1. download all .sra files from GSE##### into your SRA folder (wherever you have configured sratools to stick data).
2. produce a sample annotation sheet, PROJECT_NAME_annotation.csv, in your metadata folder
3. produce a project configuration file, PROJECT_NAME_config.yaml, in your metadata folder.

Finalize the project config and sample annotation

That's basically it! Geofetch will have produced a general-purpose PEP for you, but you'll need to modify it for whatever purpose you have. For example, one common thing is to link to the pipeline you want to use by adding a pipeline_interface to the project config file. You may also need to adjust the sample_annotation file to make sure you have the right column names and attributes needed by the pipeline you're using. GEO submitters are notoriously bad at getting the metadata correct.

A few real-world examples

geofetch -i GSE95654 --just-metadata -n crc_rrbs -m '${CODE}sandbox'
geofetch -i GSE73215 --just-metadata -n cohesin_dose -m '${CODE}sandbox'

You'd next want to run these through a pipeline like this:

looper run ${CODE}sandbox/cohesin_dose/cohesin_dose_config.yaml

or:

looper run ${CODE}sandbox/autism_microglia/autism_microglia_config.yaml -d

You can find a complete example of using geofetch for RNA-seq data.

Tips

• Set an environment variable for $SRABAM (where .bam files will live), and geofetch will check to see if you have an already-converted bamfile there before issuing the command to download the sra file. In this way, you can delete old sra files after conversion and not have to worry about re-downloading them.

• The config template uses an environment variable $SRARAW for where .sra files will live. If you set this variable to the same place you instructed sratoolkit to download sra files, you won't have to tweak the config file. For more information refer to the sratools page.