I have some MiSeq data, paired-end, and am following the MiSeq SOP.
I clearly have too many sequences - over 2million unique sequences after contig joining and basic QC (screen.seqs), and over 600k after chimera removal.
So I have been looking at trim.seqs to try and remove low quality sequences. Which brings me to my question…
Should I run trim.seqs before or after make.contigs? Can I even run it on fastq directly?
What other steps should I be taking, that are not in the SOP, that will allow me to reduce the size of the dataset?