Question regarding a comand

1

Dear Users,
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

2

The count_table file keeps track of the number of times a sequence appears in a sample. So if you are removing a sequence from the fasta file, you also need to remove it from the count_table file or you will get errors further down the pipeline.

3

Thanks Dr. Schloss. Now it is clear to me.