...

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).

...