Primer filtering with bbduk / bbduk2.sh

Latrunculia · 10-07-2016, 05:33 AM

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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10-07-2016, 05:33 AM	#1
Latrunculia Junior Member Location: Sweden Join Date: Jun 2016 Posts: 4	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