I presented my qiime analysis result in my weekly meeting. My senior asked me after the de noising (Dada2 analysis) why sample 6 has very low sequence count and he asked me is it good to take that sample for further analysis.
Before de multiplexing, sample 6 has 85523 sequence count. After de noising, sample 6 has 315 sequence count. I didn’t trim or truncate the low quality reads.
De multiplexing step (sequence count of all the sample)
After dad2 analysis
|Sample ID||Sequence Count|
This is the command I ran
qiime dada2 denoise-paired --i-demultiplexed-seqs ITSpaired-end-demux.qza --p-trim-left-f 0 --p-trim-left-r 0 --p-trunc-len-f 0 --p-trunc-len-r 0 --o-representative-sequences 2ITSrep-seqs-dada2.qza --o-table 2ITStable-dada2.qza --o-denoising-stats 2ITSstats-dada2.qza
Could you please explain me how sequence count value is determined? My opinion about sequence count is number of base pair in sequence. For Instance, Sample 6 has 315 base pair after de noising.
If I am wrong, could anyone please explain about that sequence count?
One more query is what is the minimum OTU sequence length to consider as valid OTU sequence
Thanking you in advance. Looking forward to your reply.