Overview

In the previous tutorial we ran breseq with two different options to get a feel for the type of filtering breseq does by default. Here we will visualize these differences.

Learning Objectives

• Use genome diff files to generate a comparison table to see differences between samples (or in this case different types of analysis).

Tutorial:

Breseq naturally creates numerous intermediate files and directories as it runs to facilitate picking up where it left off if the process is interrupted before it can finish. Therefore, most of these files can safely be ignored once the run is complete. The exceptions to this are the output directory (which contains the human readable files generated during the run), and the data directory (which can be used to generate additional figures for mutation determination). Information and directions for creating additional figures can be found in this shameless self promoting link. While the *.html files generated by breseq provide a good human visualization of how the mutation was called, .html files are not very useful computationally. Conversely, genome diff files are very useful computationally and human readable (although not as visually stimulating as the html files).

In our previous tutorial we sent our output to a folder titled breseq_output for both the with and without_stats conditions. Within each of these folders is a genome diff file titled output.gd that we will use to generate a new html table comparing the different mutations called in each set of conditions. The command that we will use is installed with the breseq installation in the BioITeam community resources and is can be invoked using gdtools compare. See if you can generate a file named stat_comparison.html.

gdtools compare -h

gdtools compare -o stat_comparison.html -r reference/REL606.6.gbk breseq_output/with_stats/output/output.gd breseq_output/without_stats/output/output.gd

All of the necessary files to complete our analysis have now been generated, but not in the most usable forms. In order to facilitate an easier transfer of the breseq output two small helper scripts have been placed in the $BI/gva_course/mixed_population/helper_scripts folder (export-breseq and batch-run.pl). Copy both files into the breseq_output directory and then run the export-breseq script by just typing its name from within the breseq_output directory.

cp $BI/gva_course/mixed_population/helper_scripts/export-breseq breseq_output
cp $BI/gva_course/mixed_population/helper_scripts/batch_run.pl breseq_output
cd breseq_output
export-breseq

You should now have 2 files that now need to be copied to your local computer to visualize the data: 05_Output_Export.tar.gz and stat_comparison.html. These can be opened in a web browser. Do so and explore the output!