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Old 10-07-2016, 05:33 AM   #1
Latrunculia
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Location: Sweden

Join Date: Jun 2016
Posts: 4
Default Primer filtering with bbduk / bbduk2.sh

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

Code:
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
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