The DADA2 filter excludes most of the leads.
I am a university student in Japan and a beginner in analysis, so please understand that I am not very good at this.
I am using activated sludge samples for analysis with DADA2.
However, when I use "qiime dada2 denoise-paired", I get the following results. (Photo 1)
Most of the input reads are lost at the time of filtering, and nothing remains at the end.
The forward sequence has a high quality score, but the reverse sequence has an extremely low score. (Photo 2)
The actual code used is shown below.
qiime dada2 denoise-paired \
--i-demultiplexed-seqs paired-end-demux.qza \
--p-trunc-q 0 \
--p-trim-left-f 30 \
--p-trim-left-r 30 \
--p-trunc-len-f 230 \
--p-trunc-len-r 230 \
--o-representative-sequences rep-seqs-dada2.qza \
--o-table table-dada2.qza \
--o-denoising-stats stats-dada2.qza \
--verbose
Adding "--ptrunc-q 1 " did not change the result.
I have two questions.
(1) What is the cause of the problem?
PCR? NGS? DNA extraction? Others?
(2) Can I get any result from this data?
I would like to get some results, excluding the accuracy of the data.