Open husensofteng opened 4 years ago
Actually, it turns out there can still be canonical sequences reported as not mapping in blastp. I have tested the following parameters that seem to find the matches properly: -evalue 10000 -comp_based_stats 0 -ungapped
Remove the
-max_target_seqs 1
parameter inblasp
process to avoid early stopping of the algorithm that makes it not find the top best matches.See the references here and here
https://github.com/lehtiolab/proteogenomics-analysis-workflow/blob/3472dcbaf8b3d20d41a7113519dff691c0a4b0b7/main.nf#L698