README.md

June 12, 2018 ยท View on GitHub

In this example, we will infer recombination parameters of Helicobacter pylori by using reads sequenced from a transformation experiment. We will start with a multi-sample bam file (TC1_read.bam).

  1. Follow the instruction to install mcorr and download this repository:
cd ~/Downloads
git clone https://github.com/kussell-lab/mcorr_examples.git
cd Helicobacter_pylori_transformation_experiments
  1. We then calculate correlation profiles using mcorr-bam, and perform fitting using mcorr-fit. It takes 5-10 minutes in a normal PC.
mcorr-bam NC_000915.gff TC1_read.bam TC1_read
mcorr-fit TC1_read.csv TC1_read
  1. Results:
    • TC1_read_fit_reports.txt, which shows the fitting results;
    • TC1_read_best_fit.svg, which shows the best fit;
    • TC1_read_parameter_histograms.svg, which shows the distribution of the measured or inferred parameters;
    • TC1_read_fit_results.csv, which shows the fit results in a CSV file.