using primer prospector

Objective: select good primers for sequencing a section of the mer operon.

Methods: We continued to use the script check_primer_barcode_dimers.py to test ~1000 barcodes combined with a pair of primers. Abby has list of primers tested.

The overall speed of our testing was greatly increased by using files on the Desktop of the VM running on an internal HDD. This was much faster than using files from a VM stored on an external USB 2.0 drive, or files accessed through the Shared_Folder.

Results: Every primer-barcode combination was eliminated because all pairs produced secondary structures. This seams unrealistic, leading us to believe that we are using the script wrong. This could also happen if there is conflict between our primers and Illumina adapter.

3 hours