ASGAL (Alternative Splicing Graph ALigner) is a tool for detecting the alternative splicing events expressed in a RNA-Seq sample with respect to a gene annotation. The main idea behind ASGAL is the following one: the alternative splicing events can be detected by aligning the RNA-Seq reads against the splicing graph of the gene.
The instructions to install and use ASGAL are at http://asgal.algolab.eu.
See here for more details.
git clone --recursive https://github.com/AlgoLab/galig.git
cd galig
make prerequisites
make
./asgal -g [genome] -a [annotation] -s [sample] -o outputFolder
In more detail:
# Align RNA-Seq reads to a splicing graph
./bin/SpliceAwareAligner -g [reference] -a [annotation] -s [sample] -o outputFolder/output.mem
# Convert alignments to SAM format
python3 ./scripts/formatSAM.py -m output.mem -g [reference] -a [anotation] -o outputFolder/output.sam
# Detect events from alignments
python3 ./scripts/detectEvents.py -g [reference] -a [annotation] -m output.mem -o outputFolder/output.events.csv
cd example
tar xfz input.tar.gz
../asgal -g ./input/genome.fa -a ./input/annotation.gtf -s ./input/sample_1.fa -o outputFolder
This command will produce four files in the output folder:
An extended explanation of this example can be found here.
The tool has been tested only on 64bit Linux system. You can find more information at http://asgal.algolab.eu.