Hi all, I used to use e-value <= 1e-5 for getting any meaningful blast alignment results. Just saw this statement in BLAST FAQ
"The lower the E-value, or the closer it is to zero, the more "significant" the match is. However, keep in mind that virtually identical short alignments have relatively high E values. This is because the calculation of the E value takes into account the length of the query sequence."
That makes me wondering if e-value<=1e-5 is good or too strict for illumina 90bp pair-end data with insert size ~150bp (yeah, a small bit overlapped. I just put 10 N between readA and readB for blasting)? The word short can be tricky here. Any suggestion or 'rule of thumb' kind of experience is welcome. Thanks in advanced.
