Has anyone used "common sequences" CS1_515F and CS2_806R?


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 5’ 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?

If those primers are used as the sequencing primer on the MiSeq then their sequence should not appear in your data and you should be good to go.