q-mer analysis: a generalized method for analyzing RNA-Seq data.

This repository is for the paper "q-mer analysis: a generalized method for analyzing RNA-Seq data."

1. How to use

To use q-mer analysis for the example data (example.sam), conduct the following.

./qmer example.sam example_result 10

2. How to reproduce the Figures in the paper

To reproduce, follow the jupyter notebook in qmer_cocaine or qmer_sz. Note that you need the gff file for H. sapiens to follow the notebook 1.count_based.ipynb.

3. Requirements

• python (3.7.3)
• anaconda3-5.3.1
• biopython (1.75)
• pandas (0.23.4)
• numpy (1.15.1)
• sklearn (0.24.1)
• bokeh (2.2.3)