I was going through a protocol of running MOTHUR. I found the following command:
mothur > screen.seqs(fasta=microbiome.trim.contigs.good.unique.align, count=microbiome.trim.contigs.good.count_table, summary=microbiome.trim.contigs.good.unique.summary, optimize=start-end-minlength, criteria=90, maxhomop=8)
Query: Can you tell me why this “count” option has been included? I have checked that even without “count” the output comes is same except a “.count_table” file.
Thanks and Regards