ASAS-EGB

ASAS-EGB is a library for estimating allele-specific alternative splicing events using transcriptome data.

Installation

ASAS-EGB is released as a Python package which requires Python 3.7 or higher to be installed on the computer.

To install ASAS-EGB, some Python packages that ASAS-EGB depends on should be installed first. In order to successfully compile some of the packages, several system libraries should be pre-installed. For example, on Ubuntu, these libraries may need to be installed:

sudo apt install zlib1g-dev libbz2-dev liblzma-dev

Then, use pip to install dependent packages:

pip install --user numpy scipy pandas cython
pip install --user pymc3 pyarrow
pip install --user pysam htseq

Then, use pip to install ASAS-EGB:

pip install --user asas-egb

After the installation, if you cannot run asas-egb from the terminal, this is caused by the executable binary file asas-egb not being found in the system path, you may need to run:

export PATH=~/.local/bin:$PATH

To use the plot module, matplotlib should also be installed:

pip install --user matplotlib

Example

To demonstrate the use of ASAS-EGB, an example is provided, it can be downloaded at: asas-egb_example.zip.

Unzip the file and enter the directory asas-egb_example.

Build database

asas-egb build-database -e inputs/as_events.gff3 -f inputs/genes.gff3 -a "gene_name" -v inputs/snps.vcf -C -s "NA12878" -o db

Inference

asas-egb inference -n 2 -d db -b inputs/alignments.bam -L 54 -P -M 103.46 -S 19.25 -o results

Stats

asas-egb stats -d results

Plotting

Plot in event isoform view:

asas-egb plot -d results -i "SE.1083-PHASED"

Plot in gene isoform view:

asas-egb plot -d results -i "SE.1083-PHASED" -g