Along with, percentage identity cutoff value can we also introduce query coverage cutoff value for forming groups or grouping of core genes across the genomes. Because in some genomes, it is known that a particular gene sequence is truncated so the mere presence of it gets a hit for that genome but it is a false positive hit. Therefore, is there any default query coverage set for blastp, cd_hit or usearch in roary, if so then where can we find those cutoff values or at what they are set? In case, not then how can we incorporate that in a run?
Along with, percentage identity cutoff value can we also introduce query coverage cutoff value for forming groups or grouping of core genes across the genomes. Because in some genomes, it is known that a particular gene sequence is truncated so the mere presence of it gets a hit for that genome but it is a false positive hit. Therefore, is there any default query coverage set for blastp, cd_hit or usearch in roary, if so then where can we find those cutoff values or at what they are set? In case, not then how can we incorporate that in a run?