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.
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 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
.
Run the download command to download the necessary Gene Ontology files.
java -jar sbas2go download
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.
Finally, the following command ingests das2go.tsv
and dge2go.tsv
and generates some output 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