Hi there, I have these pair of linker and primers in the demultiplexed files that I downloaded from the sequencing center.
341F - Illumina linker - 5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAG-3’ native primer 5’-CCTACGGGNGGCWGCAG-3’
Full sequence 5’-TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG-3’
806wR - Illumina linker - 5’-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAG-3’ native primer 5’-GACTACHVGGGTWTCTAATCC-3’
Full sequence 5’-GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTWTCTAATCC-3’
I have used following commands for cutadapt using the full sequence:
qiime cutadapt trim-paired
–i-demultiplexed-sequences paired-end-demux.qza
–p-front-f TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGCCTACGGGNGGCWGCAG
–p-front-r GTCTCGTGGGCTCGGAGATGTGTATAAGAGACAGGACTACHVGGGTWTCTAATCC
–o-trimmed-sequences paired-end-demux-trimmed.qza
However, when I use this trimmed.qza file for subsequent dada2 denoising step, I get extremely low percentage of passed filter and other outputs. Can you guys help me out here?
Thanks
MAN
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