I have received 16S rRNA sequencing data for ~ 100 samples.
I want to use these sequences to identify the samples to genus level using the NCBI BLAST 16s bacteria and archaea database.
For each sample I have a forward primer fasta sequence (7F) and a reverse primer fasta sequence (1540R).
For ~40 I have a 'spliced' sequence which contains a fasta with a merged forward and reverse primer data. This was provided by the sequencing company. ~60 samples do not have a 'spliced' sequence.
My questions are:
1.) Is there a best practice protocol for merging forward and reverse primers?
2.) Can I concatenate the forward and reverse primer sequences into a single fasta file and search using these, or will this introduce biases?
3.) For the sequences that were not spliced, should I favour one of the two primers for identification purposes?