mothur

Single end read alignments

I have a data set of single end reads based on the 16S v4 region. The reason they’re single end is I only have access to an iSeq instrument with 2x150 bp reads and the 16S v4 region nears 300 bp including primer sequences.

I’ve managed to process the data using the miseq protocol with some adjustments for a single fastq file (namely, using fastq.info and make.group commands). This works great. My question is about the post-alignment screening portion of the protocol. So far I’ve prepared a pipeline that screens the F primer fragment of the amplicon for alignment using start=11895 and end=21278, but I imagine this excludes the R primer fragment from analysis. Does it make sense to analyze each fastq file twice, once for the F fragment (start=11895 and end=21278) and again for the R fragment (start=21340, end=25434)? Or am I not thinking about this correctly.