Hi Mothur community,
I would like to know how does the command seq.error works. I didn’t find much information about that on the wiki page for this command.
My question arises from this story:
The quality of my sequences is rather poor, especially towards the end; however, I have a lot of sequences more than I need. Thus, prior to start the processing with Mothur SOP, I applied a quality filter that removes the sequences with an expected error over a certain threshold (based on the quality scores). To test if this approach is effective, I applied the mothur SOP to the Mock community sample with or without this filtering, until I reached the “assessing error rates” step. I calculated the rarefaction curve and the error rate for the two. The slope of the two rarefaction curves is remarkably different, this, as far as I know, meaning that the filtering works. However, the error rate is the same (high!).
I feel that knowing better how the error rate is calculated could help me to understand this discrepancy.
Thanks a lot!