I am working with 16S sequencing data generated using 515F-806R primers.
What is the difference between adapter and front in
qiime cutadapt trim-paired?
I got the following cut adapt parameters from a colleague that generated his 16S in the same DNA core that I did using the same primers. However, I am confused about the differences between adapter vs front and I am not sure if he used the correct sequence for each parameter.
qiime cutadapt trim-paired\ --i-demultiplexed-sequences paired-end-demux.qza\ --p-cores 10\ --p-adapter-f ATTAGAWACCCBDGTAGTCC\ --p-front-f GTGCCAGCMGCCGCGGTAA\ --p-front-r GGACTACHVGGGTWTCTAAT\ --p-adapter-r TTACCGCGGCKGCTGGCAC\ --o-trimmed-sequences trimmed-paired-end-demux.qza
In his code, the 515F sequence was entered in
--p-front-f, and 806R sequence in
--p-front-r. From what I could gather, an index sequence primer (ATTAGAWACCCBDGTAGTCC) was entered in
--p-adapter-f and 515 reverse sequence (TTACCGCGGCKGCTGGCAC) was used for
I found it odd to have an index sequencing primer specified on
--p-adapter-f and then the 515 reverse on ‘–p-adapter-r’. Is this correct?
From what I’ve read, I am with the impression that there is no real difference between adapter and front, and that they are just two similar options to remove different primers from the 5’ or 3’ ends. Am I too far off?
Thanks for your attention. I’m looking forward to your reply.