Ben Wu

Having this problem as well, for some reason fastq-multx is not recognizing the barcode correctly.

Sure, Illumina Miseq, paired ends. R1 forward and R3 reverse sequences. ``` /Users/###/miniconda2/bin/fastq-multx -B /Volumes/homes/###/SRA/Columbia.Gut.Murine/map/reversecomplement/reversecomplement.txt /Volumes/homes/###/SRA/Columbia.Gut.Murine/2_fastq/lane1_NoIndex_L001_R1_001.fastq /Volumes/homes/###/SRA/Columbia.Gut.Murine/2_fastq/lane1_NoIndex_L001_R3_001.fastq -o /Volumes/homes/###/SRA/Columbia.Gut.Murine/SRA/R3/R3.%.fastq /Volumes/homes/###/SRA/Columbia.Gut.Murine/SRA/R3/R1.%.fastq ``` ``` /Users/###/miniconda2/bin/fastq-multx -B /Volumes/homes/###/SRA/Columbia.Gut.Murine/map/forward/forward2.txt /Volumes/homes/###/SRA/Columbia.Gut.Murine/2_fastq/lane1_NoIndex_L001_R1_001.fastq /Volumes/homes/###/SRA/Columbia.Gut.Murine/2_fastq/lane1_NoIndex_L001_R3_001.fastq -o /Volumes/homes/###/SRA/Columbia.Gut.Murine/SRA/R1/R1.%.fastq -o...

I am also using: Version: 1.3.1 Here is cat of the fastq file ``` + AAAAAFFAA11>AEGGGFGCGGHGGGAEHHFHHGHHEGGGHH1B01BF/BFEGCEE@/B2222BFFFF1BEFACEHF1B@/EEGEE