smartSim: Simulation of splice aware single cell Smart-seq3 data

Prerequisites

In order to use this package: you need folowing software:

• conda (https://www.anaconda.com/)

We provide a conda environment, which can be created with:

conda env create -f smartSim_env.yml

Input

• reference gtf file
• reference fasta file
• aligned and barcoded Smart-seq3 data similar to the data you want to simulate (alternatively you can use example_data/aligned)

Usage

We provide a tutorial to simulate reads using the example data: tutorial.R