I am remapping buffalo SNPs thorough UOA_WB_1 genome assembly. Buffalo SNPs have previously been mapped against cattle reference genome assembly (UMD3_1).
Now, I am looking for an outline to filter out the results, but I do not know the right framework (e.g., %identity, e-value, alignment length, mismatches, bit score, etc)!
Can anyone help me with this?
There is no one way to do it, as every metric you listed is important in different contexts. Since BLAST is a heuristic algorithm it won't give a single 'best' answer, either. Generally speaking, it uses the e-value/bit score as the first ranking method, but you can easily change that depending on the parameters you use when you run it. The best way for you to decide your ranking method is to determine which is/are more important for you after you've aligned your SNPs.
I find the wiki page for BLAST (https://en.wikipedia.org/wiki/BLAST) is a good primer to understand how it determines matches, which should help you figure out what's most important for you.
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