Maybe a silly question for expert bioinformaticians, but I cannot figure out how to make stacks (v. 1.39) to recognize my combinatorial barcode file (3 columns file: barcode 5bp, index 6bp and sample name). Every time I run the command I receive an error message saying "Too many columns (3) specified in '/home/carol/RADseq/Barcodes/all_index-barcode' for single-end barcodes on line 1." Can someone help me to figure put the problem?
The command I have used is: ./process_radtags -i fastq -P -1 /home/carol/RADseq/Lane1_NonDemultiplexed/Lane1_read1.fastq -2 /home/carol/RADseq/Lane1_NonDemultiplexed/Lane1_read2.fastq -b /home/carol/RADseq/Barcodes/all_index-barcode —-index_inline —-barcode_dist_2 —-retain_header -o /home/carol/RADseq/Demultiplexed_Sequences/Demult_all_2ndtry -e pstI -D