Workflow and minor bugs

[dnbenso]

Hi

I'm working with some people who are interested in utilising this software on larger polyploid species, and I was hoping for some guidance on how you would use the tools in a real world example.

I managed to run CROPSR.py on a wheat genome (with some minor changes related to cpf1) and produce the large CSV file. I've been able to run the prmrdsgn2.py (after renaming the functions import) on the sample data with a small fasta sequence. I'm not really sure on the outputs expected here? - a markers.txt file?

What other modules are there for analysis?

Thanks very much in advance for your time.

Cheers
Derek

[H2muller]

Hi Derek,

Thanks for reaching out. I'd like to start by advising you that the CPF1 model is currently unsupported because we have no scoring algorithm implemented for it. If you decide to use it at your own discretion, please be advised that we can't guarantee the success of the designed guides at this moment.

Currently, the prmrdsgn2.py module is written to take a single gene (or fragment) FASTA file as one of the inputs, and the whole genome FASTA as a second input, and the outputs are the resulting alignment files from BowTie. We are currently working on a new implementation for that module to address some performance issues that prevent it from working on the full database (either in CSV or in a different database structure) in a timely manner.

I would be interested in learning what other kinds of modules you would find helpful on your research, so we can study the viability of implementing them.

Best wishes,
Hans