Hi,

How comes the barcode not be at 5' or 3' end, do you have primer sequences or stuff like that ? The barcode you show cannot be found in the sequence you show...
I know that FastqMCF is an alternative tool that can be found in the toolshed and that deals with barcode.

Philippe

2012/12/3 Rajarshi Ghosh <rajarshi@princeton.edu>
TCGCAGGA