#The command to run trim2bRAD_2barcodes_dedup.pl is complicated, so
#another script -- 2bRAD_trim_launch_dedup.pl -- is used to generate the command for us:
2bRAD_trim_launch_dedup.pl cat.fastq > dedupCommands
#look at the commands file
cat dedupCommands
#returns our next commands to execute:
trim2bRAD_2barcodes_dedup.pl input=A_CTGCAG_R1.fastq site=".{12}CGA.{6}TGC.{12}|.{12}GCA.{6}TCG.{12}" adaptor="AGATC" sampleID=100
trim2bRAD_2barcodes_dedup.pl input=B_GAAGTT_R1.fastq site=".{12}CGA.{6}TGC.{12}|.{12}GCA.{6}TCG.{12}" adaptor="AGATC" sampleID=100 |