While filtering illumina MiSeq data I want to check whether the forward primer matches the beginning of each read (these are single-end reads). Lots of programs let you do this, but then they trim off the primer sequence. I'd actually like to keep the primer sequences in, but throw out any reads that don't have the primer sequence.
*Edit: note that degenerate primers were used, so there are multiple sequences that could be matched.
Does anyone know of a way to do this with fastq files? Ideally I'd like to use Trimmomatic's ILLUMINACLIP command, but I haven't figured out a way to stop it from clipping the sequence.
The mothur command "trim.seqs" does this for fasta files (when keepforward=T), but I'd rather not have to waste time converting between fastq and fasta since this is a pipeline I will need to re-run a lot.
Thanks in advance!