I am new to 16s sequencing and Mothur as well. I run a 2x250bp Miseq paired ends run, amplified V4 region. Could anyone tell let me know:
- How to tell if my 16s raw data needs trimming of sequence adapters, barcodes, linker, and 16s primers?
- If trimming is necessary, how this is normally done in mothur?
- 16s primers are degenerate primers that contains N, V. M. Will this be a problem when it comes to trimming?
- How do I evaluate the quality of trimming?
Thank you very much. If similar questions have been asked in the past, any links would be appreciated.
All the best!