I am a beginner for Qiime2 and after reading the tutorials I started analyzing my data. I got OTU table after applying Dada2 pipeline and I noticed that merging for most of the samples have failed . As a result I lost most of the samples from otu table. Could you please provide your expert opinion on improving the parameters for getting all samples.
I used following commnads
qiime dada2 denoise-paired --i-demultiplexed-seqs demux.qza --p-trim-left-f 25 --p-trim-left-r 20 --p-trunc-len-f 300 --p-trunc-len-r 300 --p-max-ee-f 2 --p-max-ee-r 2 --p-trunc-q 2 --p-chimera-method consensus --p-min-fold-parent-over-abundance 1 --p-n-threads 1 --p-n-reads-learn 1000000 --p-hashed-feature-ids True --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza
Another point is that I also have demultiplexed and mergepair reads for each sample as provided by the sequencing company. Can I use these prejoined and demultiplexed fastq files for Dada2 pipeline. If yes, then
- what parameters I shall consider in Dada2 pipeline so as to avoid merging?
- For importing fastq manifest files of these in qiime 2 shall I use “input-format SingleEndFastqManifestPhred33”?
Thanks for your help.