I have a fastq sequence file (have both multiplexed and demultiplexed files) from ion torrent.In total there are 192 samples in the sequence with 2 barcodes (16s and ITS). 96 samples with 16s primer and 96 samples with ITS primers and both the 16s and ITS primers are attached to the same barcodes. I find it difficult in Qiime 2 to import or analyse the data. In Qiime1 I can just change the primer sequence in mapping file and either 16s or ITS primers get excluded. Is there a simiar method to do this in Qiime2 as well?
Is it possible to separate the sequence file based on primers and do the downstream analysis. I have been trying different methods but couldn’t able to figure out.
Kindly advise how to proceed with my sequence data.