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
).
- 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
- We then calculate correlation profiles using
mcorr-bam
, and perform fitting usingmcorr-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
- 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.