Magic blast -score parameter
The only mention anywhere that I have forunf for the magicblast -score parameter is this:
The alignment cutoff score (-score option) can be expressed as either a constant or a function of read length in this format: L,b,a for a * length + b
Where for long reads:
r >= 200 score threshhold: 120
But what does the score value mean? What is best possible score? A high or low number? If I want to allow 1nt mismatch for 150nt reads what would I set the score to?
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