Overview:
Learning Objectives:
Tutorial Running Breseq on SSCS and Trimmed Reads:
The following reference files should be copied from the $BI/gva_course/mixed_population directory into your reference folder: 1400flanking.gff3, and REL606.maksed.gff3.
Just like the previous tutorial if these commands are run on an idev shell they should be run in the background so both comparisons can be run at the same time. Alternatively they can be submitted to the que outside of an idev shell.
In this case we are going to be running breseq in both polymorphism mode, and targeted sequencing mode. We will also be using 2 different reference files, 1400flanking.gff3 should be used as a standard reference while REL606.masked.gff3 should be used as a junction only reference. Also we want to make good use of the 12 processors we have available so 6 processors should be used for each sample.
Again, just like the previous tutorial we now want to create a comparison file using "gdtools compare" so we can see the difference of having the trimmed reads vs the SSCS reads. This time you want to create a file "trimmed_vs_SSCS.html".
The comparison table as well as the output for the trimmed and SSCS reads can now be exported to your local computer for viewing. If you don't remember how to do that, check back here one of the previous tutorials.