I have to analyze PacBio transcriptome data with four bin sizes: 1-2 Kb, 2-3 Kb, 3-6 Kb and 5-10 Kb. I can understand that the HSP length cut-off and HSP-Hit coverage settings must be customized for each of the bins for running Blast but what should be the criteria for the same. Any good literature or suggestions on this topic will be of great help.
Abhishek Kumar
it is like trial and error. try different values, like 33%, 50% and 75% of total length, once you play arround you will come up with criteria of optimal HSP length.
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