Benchmarking BleTIES with Tetrahymena read data

MIC enrichment from Tetrahymena thermophila, used to test performance of BleTIES with both PacBio Sequel I subreads and Nanopore MinION long reads, and compared against published IES sequences.

This repository supplements our preprint describing the BleTIES software.

Source data and setup

Read metadata are listed in files read_*_data.tsv.

Run script download_data.sh to prepare directories and download reads and reference genomes.

Install BleTIES with Conda:

git clone git@github.com:Swart-lab/bleties.git
conda env create -f bleties/env.yaml -p ./envs/bleties_env
conda activate ./envs/bleties_env
cd bleties
pip install .

Analysis

Run script do_bleties.sh to map long reads to reference MAC genome with minimap2, and use BleTIES to reconstruct IESs. Edit script to specify paths on your system.

Analysis is documented in the following Jupyter notebooks:

• Compare_BleTIES_PacBio_Nanopore_predictions.ipynb - Main notebook
• Check_reported_intragenic_IESs.ipynb - Check whether intragenic IESs reported by Hamilton et al. (2016) are also assembled by BleTIES
• Clips_vs_inserts_at_non-predicted_IESs.ipynb - Look for clips/inserts at known IES junctions where BleTIES did not predict an IES