phrap - turn off trimming?

isaac isaacjunk at hotmail.com
Wed Apr 3 05:29:07 EST 2002


Esp. with small assemblies of just a few reads, phrap has the nasty
habit of trimming off the first 30 bases or so off the ends if there
is only a single read's evidence at that position.  Is there a way to
turn off trimming completely?

As our workaround, we actually duplicate the entries in the fasta file
while appending an "n" at the start and end of each copy ( or else
phrap will say it's a duplicate and toss it out ).  This allieviates
the problem a lot, but not completely.

Isaac

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