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Old 07-17-2012, 12:38 PM   #2
JackieBadger
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Location: Halifax, Nova Scotia

Join Date: Mar 2009
Posts: 381
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You can use PRINSEQ http://edwards.sdsu.edu/cgi-bin/prin...seq.cgi?home=1
As far as I remember you can tell the program to trim a certain amount of bases from either end.
You can also do this with Galaxy: https://main.g2.bx.psu.edu/

Prinseq may be better as you will retain your Q data.

If you wanted to sort your amplicons while you remove primers and adapters you could use jMHC http://code.google.com/p/jmhc/
For this you need to know your primer sequence but you should be able to figure out what your primers were from your sequence.
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