Hi
I am using BLAT for mapping sequences of different length ranging from
oligos to a complete gene sequence. For small sequences I am using your
recommendation from http://genome.ucsc.edu/FAQ/FAQblat.html website for
short sequences. As I go towards higher level of annotation for example est
sequences or ensemble gene sequences, I am getting multiple hits(too much to
handle) with default BLAT parameters.
I was wondering if you know of any correpondence between the query sequence
length and the score/identity generated by BLAT(I followed your instruction
to generate score and identity from the psl file). For example, which blat
score is acceptable for sequence length 100 or 1000 or 10000. I am
interested in the best alignment or n-best alignments and not all.
thanks and regards.
Fahim
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