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

Join Date: Jun 2016
Posts: 4
Default 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?


Latrunculia is offline   Reply With Quote

bbduk, bbduk2, illumina, trimming

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