Denoise using dada2 for paired end

I am Jihan and I am new with bioinformatics and I am using QIIME2 version qiime2-2018.11.
Now I am in the step of denoise using dada2 but my question is this command for single-end and if so what about paired-end using this command
qiime dada2 denoise-single
–i-demultiplexed-seqs demux.qza
–p-trim-left 0
–p-trunc-len 120
–o-representative-sequences rep-seqs-dada2.qza
–o-table table-dada2.qza
–o-denoising-stats stats-dada2.qza
As you see above command its used for single-end, what about paired-end for ITS sequences

Please could anybody can help.


Hi @Abdullah1,
Welcome aboard!

To use DADA2 for paired-end reads check out the documentation for dada2 denoise-paired here, you can also get these help files in any qiime2 command by adding the --help tag after whatever action you’re interest in. That being said, since you are using ITS sequences, have a look through this new tutorial specific for ITS amplicons as it covers some important and ITS-specific points that should be considered.
Hope that helps!

1 Like

This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.