#Command to run Comet on file 09
runCometQ 2015_May_26_Geoduck_09.raw

#command to run trans-proteomic pipeline after Comet searches
#example is given for file number 09
#the text after -N will be included in the output file name interact-2015_May_26_Geoduck_09.pep.xml or prot.xml
#the input file is 2015_May_26_Geoduck_09.pep.xml
xinteract -p0.9 -OAp -N2015_May_26_Geoduck_09 2015_May_26_Geoduck_09.pep.xml