My apologies if this is the wrong board to post this question. I am quite a novice with Mothur, but I did use it about a year ago to analyze 16s rRNA sequencing data using the MiSeqSOP. Previously, I used primers 515F and 806R and everything went smoothly. I am doing a similar analysis on a new data set, and now the only difference is that I used primers CS1_515F and CS2_806R. These CS regions are referred to as common sequences. Here is a description of the CS: The primers contained 5â€™ common sequence tags (known as common sequence 1 and 2, CS1 and CS2) as described previously (e.g. Moonsamy et al. 2013). The forward primer, CS1_515F (ACACTGACGACATGGTTCTACAGTGCCAGCMGCCGCGGTAA) and CS2_806R (TACGGTAGCAGAGACTTGGTCTGGACTACHVGGGTWTCTAAT) were synthesized by Integrated DNA Technologies (IDT; Coralville, Iowa) as standard oligonucleotides. I believe these CS regions serve a linker or barcode function for sequencing, but I may not be absolutely correct on that.
My main question/concern is the possibility that these ~20 bp CS regions would cause problems when it comes time to align sequences or run them against a bacteria database using the rdp training set and silva bacteria set. Just curious if anyone has used these sequences before, and if there is a way to cut off the CS region while analyzing them?