config.cfg

ZIPPED=yes
FILENAMES=/mnt/brick2/justin/20150901/Lane_1_NoIndex_L001_R1_001.fastq.gz,/mnt/brick2/justin/20150901/Lane_1_NoIndex_L001_R2_001.fastq.gz,/mnt/brick2/justin/20150901/Lane_2_NoIndex_L002_R1_001.fastq.gz,/mnt/brick2/justin/20150901/Lane_2_NoIndex_L002_R2_001.fastq.gz
GENES rpob_utr,rpoz,cspe
BARCODE_LENGTH 14
FORWARD_ALIGN_SEQ CTGGGTATCAACATCGAACTG,TCATGCCCAGTCATTTCTTC,AAATCACTAACGGTGCCAAAG
REVERSE_ALIGN_SEQ AAAGATT,GCGCGTCGCGCT,GGTTGAGG
TARGET GAAGACGAGTAATTCTCGCTCAAACAGGTCACTGCTGTCGGGTTAAAACCCGGCAGCGGATTGTGCTAACTCCGACGGGAGCAAATCCGTG,ACCTGTGGAGCTTTTTAAGTATGGCACGCGTAACTGTTCAGGACGCTGTAGAGAAAATTGGTAACCGTTTTGACCTGGTACTGGTCGCC,GCCCTTCTGCTGCAAACGTAATCGCTCTGTAAGATACGTCAGCAAGAATTCAAAACCCGCTTAATCAGCGGGTTTTTTTTGGTCTTTAGTGTGC
THRESHOLD_OF_IMPORTANCE 3
MAX_PHASE 4
PHASE_SHIFTS_REV_TO_FORWARD 0:3|1:2|2:1|3:0,1:4|2:3|3:2|4:1,1:4|2:3|3:2|4:1