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I am doing some experiment using BowTie and WHAM which are short read aligners that aligns short DNA sequences (reads) to the human genome. In WHAM, it is specified that for 75 bps reads, it is biologically required to allow matching with two errors and if the read length increases, allowed mismatch errors should increase. Now, I want to experiment with those two tools on 150 bps. Can anybody help me what should be the allowed matching errors for 150 bps or where can I find information about it ? Actually, I want information about, "maximum tolerated miss match errors" which is biologically relevant or for various (specially 150 bps) read length. I became confused because of this list of aligners, which has varied "maximum tolerated miss match errors". Can anybody please help me about this ? Thanks in advance.
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