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-   -   Primer filtering with bbduk / bbduk2.sh (http://seqanswers.com/forums/showthread.php?t=71890)

Latrunculia 10-07-2016 06:33 AM

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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