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Latrunculia 10-07-2016 06:33 AM

Primer filtering with bbduk /

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

Code: in=16S_analysis/XXX.fna \
                        minkmerhits=2 \
                        k=17 \
                        copyundefined \
                        rcomp=t \
                        hammingdistance=1 \
                        outm='16S_analysis/with_Primer.fasta' \
                        out='16S_analysis/no_F_Primer.fasta' \
                        overwrite=true \

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?



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