Differential usage isoform benchmarking analysis

Simulation

--dir - path where simulation file will be written to

--type - "pair" or "single" ended

--rep - number of replicates

--depth - sequencing depth

--noise - background noise (the ratio of genes that remain unchanged across conditions)

bash ./simulation/mknewdir.sh --dir mame_of_dir --type pair --rep 4 --depth 5000000 --noise 0

Run analysis

--config - path to the config file

--name - the name of directory where results will be written to

bash main_script.sh --config /nfs/proj/is_benchmark/paired4_config.sh --name name_of_dir