Hi,
First of all, thanks for an excellent tool! I've had great success in genotyping Atlantic salmon using this, with some minor changes. I believe the "Tidyverse" R package is missing from dependencies. This resulted in errors in my genotyping without any errors reported whenever the clustering step was performed, in the majority of cases leading to non-obvious genotyping errors. I fixed this by independently loading the module. I may be incorrect, but I don't think the built-in test runs the clustering steps, meaning this missing dependency will not be apparent unless running with other data with additional verification steps.
Just adding some notes for others who wish to use this tool for non-human genotyping:
Change built-in look-up sequences to those from your species of interest.
Swap alignment algorithm to the built-in Matcher option. This could be a specific issue with Atlantic salmon PRDM9 sequences, but BLAST did not work correctly.
If running in bulk: Set img file in batch script instead of pulling a new container for each run.
Consider modifying ZnF array length ratio rules. This will likely be different between PCR/sequencing runs and inherent length differences in species.
Thanks again! This tool has been essential for me, and shows promise for use in all species with PRDM9 :)
Hi, First of all, thanks for an excellent tool! I've had great success in genotyping Atlantic salmon using this, with some minor changes. I believe the "Tidyverse" R package is missing from dependencies. This resulted in errors in my genotyping without any errors reported whenever the clustering step was performed, in the majority of cases leading to non-obvious genotyping errors. I fixed this by independently loading the module. I may be incorrect, but I don't think the built-in test runs the clustering steps, meaning this missing dependency will not be apparent unless running with other data with additional verification steps.
Just adding some notes for others who wish to use this tool for non-human genotyping:
Thanks again! This tool has been essential for me, and shows promise for use in all species with PRDM9 :)