[Bioperl-l] Assembling scaffold-specific est contigs (blat)

[Charles Hauser]

I have a collection of ests which I have 'mapped' onto genomic scaffolds
using blat and want to assembling these for each scaffold.

I ran blat using qual-trimmed (lucy) est seqs with blat %iden at .97 to
weed out spurious matches.

I am tempted to now use the full est sequence (not qual-trimmed) for
assembly as a lot of our reads (5', 3') have little overlap.  Anyone
have experience doing something similar?

Charles