Hi,
Thank you for your response. With certain posts on the forum, [Importing and Demultiplex process for 4 Fastq Files: R1, R2, Index1 and Index2]) I understood it is possible with the previous version QIIME1. But I am stuck at the construction of mapping file step with dual barcodes.Could you please let me know how to construct the mapping file with both barcode sequences.
Also, may I know the best pipeline to demux these files other than qiime.
Thanking you,
Rama.