cDNA Vector trim.
Phillip San Miguel
pmiguel at purdue.edu
Thu Mar 20 15:16:47 UTC 2003
David Martin wrote:
>On 20/3/03 2:47 pm, "Matthew H. Bemis" <bemis at io.iol.unh.edu> wrote:
>>Thanks for the advice! The programs work great. Now I have all this data
>>and I have phred( phd.1 ) files that I'd like to align and look for
>>mismatches( high score mismatches ). Is there software for this?
>>I have four file types to work with here:
>>if there software out there for looking for high quality mutations?
>>writing software is not out of the question for me either. I am a cs
>>graduate student, but I'd rather not re-invent the wheel.
>>thanks in advance!
>Checkout the staden package which does all sorts of things you would find
>useful, in particular pregap4 and gap4.
If you have the phredPhrap package already, you might find cross_match
sufficient. Convert your phd files to a fasta and qual files using
phd2fasta. When you do the comparsion with cross_match, a large table of
the quality values of the mis-matches is generated. Not sure if it is
what you are looking for. I generally am looking for ways to filter out
this output. Help is at www.phrap.org.
Purdue Genomics Core
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