> 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.

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