sbas2go

This app is intended to use phenol library code to perform Gene Ontology analysis on differentially expressed and differentially spliced genes from the sbas2go project.

Setup

Building the app

Clone the application from GitHub and use maven to build the app. (Note that currently we use a develop version of phenol 1.4.2-SNAPSHOT that needs to be installed locally).

git clone https://github.com/pnrobinson/sbas2go.git
cd sbas2go
mvn package

This will generate the app in the target subdirectory. We assume that you have put the app on the PATH for the following commands.

Download the sbas files

Download the sbas files from the project zenodo repository. For this analysis, we only need the following three files:

as.tar.gz
dge.tar.gz
fromGTF.tar.gz

Unpack all three files in the same directory. This app expects to be passed the path to that directory as -s,--sbas.

Download the GO files

Run the download command to download the necessary Gene Ontology files.

java -jar sbas2go download

Running the app

Following this, simply enter

java -jar sbas.jar go -s  <path/to/sbas/directory>

This outputs two files, das2go.tsv and dge2go.tsv with significant GO terms per tissue.

Output summary files

Finally, the following command ingests das2go.tsv and dge2go.tsv and generates some output files.

BED Files

To outout BED files with significant and control DAS exons, enter

java -jar sbas.jar bed -s  <path/to/sbas/directory>

This command outputs das-significant.bed and das-control.bed