Hello everyone. I'm working in a metagenomic study using a short rbcL marker as barcode. I used Illumina Miseq for sequencing and I made the routine processes for denoising and filtering Illumina reads. I picked OTUs using a 97% of cutoff value. I've got approximately 8000 OTUs in all my dataset. Each OTU has an read value, and I filtered OTUs by read number, removing OTUs with one single read and keeping the rest. I think that I could remove more OTUs taking into account the number of reads. Anyone knows if is there a cutoff value for filter OTUs.
Thank you very much for your answers.
you can define minimum cluster size. Normally it is 2. If you increase this (lets say 5), you will get fewer reads which have minimum occurance of 5 times in your dataset.
Use one script "filter_otus_from_otu_table.py" in QIIME pipeline. You can find the detailed description at http://qiime.org/scripts/filter_otus_from_otu_table.html.
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