Post date: Jan 09, 2015 5:50:4 PM
I set up a callosobruchus subdirectory within data. It has a subdirectory for gbs data where I have copied the raw sequence data and will store the parsed data and assemblies. There are five fastq files, one for gomp004, one for gomp005, and three (the original and two redos) on gomp003. I am parsing the barcodes for all five of these:
cd /labs/evolution/data/callosobruchus/gbs/
perl Scripts/parse_barcodes768.pl Barcodes/barcodes_gomp003.csv Sequences/gomp003_NoIndex_L004_R1_001.fastq
perl Scripts/parse_barcodes768.pl Barcodes/barcodes_gomp003.csv Sequences/gomp003_NoIndex_L005_R1_001.fastq
perl Scripts/parse_barcodes768.pl Barcodes/barcodes_gomp003.csv Sequences/gomp003_L008_R1_001.fastq
perl Scripts/parse_barcodes768.pl Barcodes/barcodes_gomp005.csv Sequences/gomp005_NoIndex_L007_R1_001.fastq
perl Scripts/parse_barcodes768.pl Barcodes/barcodes_gomp004.csv Sequences/gomp004_NoIndex_L006_R1_001.fastq
I am not sure where I will really want to include the original gomp003.