BIISQ
Bayesian nonparametric discovery of Isoforms and Individual Specific Quantification with BIISQ
Installation
Requires python version 2 (2.7+)
installation of required packages
Required packages: joblib cython numpy scipy
for an existing installation of python/anaconda
If you have a working anaconda or python installation, then:
pip install --user numpy
pip install --user scipy
pip install --user joblib
pip install --user cython
for a new installation of Python 2 (2.7+)
If you would like to install via a new vitual environment, then:
VIRT_HOME=/n/fs/biisq/virtenvs
cd $VIRT_HOME
virtualenv biisq_env
source biisq_env/bin/activate
pip install numpy
pip install scipy
pip install cython
pip install joblib
installation of BIISQ
git clone https://github.com/bee-hive/BIISQ.git
cd BIISQ/examples/ex_gene_1/
sh ex_gene_1_run.sh
cd viz
sh run_viz.sh
there is another example for paired end data in BIISQ/examples/paired_end.
Running this script will summarize transcript composition and quantification. By default results will be stored in BIISQ/examples/ex_gene_1/output. The summary.html file contains descriptions of the individuals and isoform compositions.
Running recommendations
If your data is very small, you might consider running BIISQ several times without proposals and merging, e.g. --max-n-prop 0 --min-n-prop 0