I have paired reads 16S of V3- V5 with length 600pb.
What is the best parameters for denoise in dada2.
I put this parameters:
qiime dada2 denoise-paired --i-demultiplexed-seqs demux-ratones-paired-end.qza --p-trunc-len-f 294 --p-trunc-len-r 274 --o-representative-sequences rep-seqs-dada2.qza --o-table table-dada2.qza --o-denoising-stats stats-dada2.qza
Thanks for the support!
Picking trim/truncate parameters for DADA2 can be a bit tricky because there is so much to consider with regards to your data/samples and there is no one right answer for all situations. Luckily the topic has been discussed extensively on the forum and I would suggest start by searching and reading a few of those to see how others are picking them. If you still can’t decide or figure out how to decide let us know and we’ll help you through it.
One good starting post is here which describes the DADA2 process and a few important considerations such as min overlap, removing nonbiological sequences etc.
Thank you, i will revise it.
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