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Old 08-04-2009, 04:05 PM   #2
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Location: Australia

Join Date: Sep 2008
Posts: 8


AFAIK you only use the -s, -q or -x options if you want only one of the files. To get all three you only need to use the -o option to set the output name (if you want) and then the names of the sff files. You have to manually rename the xml file afterwards however. e.g "sff_extract -o proj_in.454" should output "proj_in.454.fasta, proj_in.454.fasta.qual and proj_in.454.xml"
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