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
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
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
thanks!
Fabian