Primer filtering with bbduk / bbduk2.sh

[Latrunculia]

Hello,

I have merged Illumina reads and try to filter out all reads that have both, a recognisable fwrd and a recognisable reverse primer and then to trimm those primers.

And I'd like to do this in as few commands as possible.

So far I am using the following code for filtering. Note that if I specify a restrictleft & restrictleft argument no primers are found for some reason

bbduk2.sh in=16S_analysis/XXX.fna \
                        fliteral=CCTACGGGNBGCASCAG,GACTACNVGGGTATCTAATCC \
                        minkmerhits=2 \
			k=17 \
			copyundefined \
			rcomp=t \
			hammingdistance=1 \
			outm='16S_analysis/with_Primer.fasta' \
			out='16S_analysis/no_F_Primer.fasta' \
			stats='16S_analysis/Primer_stats.txt'\
                        overwrite=true \
			-Xmx6g

I can now take this file a search for the foward primer, trimm with lliteral and then do it for the reverse primer. But this is not ideal. Can it be done in one step?

thanks!

Fabian