I’m a beginner of qiime2, and I’m practicing processing a batch of bacteria data. But after dada2, there are some problems. First of all, I import the data optimized and spliced by sequencing company as single ended data.
qiime tools import --type “SampleData[SequencesWithQuality]” --input-format SingleEndFastqManifestPhred33V2 --input-path manifest.txt --output-path demux_seqs.qza
demux_seqs.qzv (290.0 KB)
Due to the optimized data and the high quality of the sequence displayed in the quality interaction diagram, I ran the following code to do dada2 without cutting.
time qiime dada2 denoise-single --i-demultiplexed-seqs demux_seqs.qza --p-trunc-len 0 --o-table table.qza --o-representative-sequences rep_set.qza --o-denoising-stats stats.qza --p-n-threads 0
table.qzv (457.6 KB) rep-seqs.qzv (334.6 KB) stats.qzv (1.2 MB)
The above is the visualization file I got after running. But the mean length is 184, and most of the sequences are less than 200. This is far from the effective length reported by sequencing company, which is about 440.
Why does this happen?
Is it because there is something wrong with the parameter setting when I use dada2? What is the appropriate parameter?
If I ignore this problem and continue with the follow-up analysis, is the analysis result useful?
I look forward to your answer and sincere thanks.