I have from MiSeq FASTQ files, pair-end, of 16s bacterial amplicons. I want to start a metagenomics analysis and I have read that most of the time people use Mothur or Qiime.
But for example Qiime needs the FASTQ files and also mapping file. My case is that I have only the R1 and R2 pair-end files for each sample which are already demultiplexed (from MiSeq) with removed barcodes and primers.
So was wondering how can I proceed from what I have already?