The PAM TTTN for the cpf1 case needs to match at the beginning of the target sequence, not the end (as is the case with NGG for cas9). We should double check this by looking at some results from both the old and the new web apps.
So the kmers generated by generate-kmers should take this into account. The command has a --start flag to take care of this. This needs to be put into effect for the cpf1 case as far as the snakemake workflow is concerned.
The PAM
TTTNfor thecpf1case needs to match at the beginning of the target sequence, not the end (as is the case withNGGforcas9). We should double check this by looking at some results from both the old and the new web apps.So the kmers generated by
generate-kmersshould take this into account. The command has a--startflag to take care of this. This needs to be put into effect for thecpf1case as far as the snakemake workflow is concerned.