I have one more question about the "Anchor length". For a RNA-seq read mapped on the splicing junction under the 0 mismatch condition, if 5 nucleotides of one end map on one exon, does it mean the rest part of the read must map on the adjacent exon? What I want to understand is that, although reducing "Anchor length" may reduce the reliability of mapping on one end/exon, but the increased number of mapped nucleotides on the adjacent exon may increase the reliability of mapping. Does it mean overall the reliability of mapping is not changed?
No, in general the probability of mapping 5 bases + (N-5) remaining bases incorrectly is higher than mapping 8 bases + (N-8) bases incorrectly because (a) there are more matching 5-mers than 8-mers in a genome and (b) there can mismatches when mapping the remainder.
J.