Overview

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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

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• 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).

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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  directory and then run the export-breseq script by just typing its name from within the breseq_output directory.

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You should now have 2 files that now need to be  to 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!