Dada2 sequence count query

Hello, All

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)

sample-12 318689
sample-10 316279
sample-9 309068
sample-4 282897
sample-8 268205
sample-7 216594
sample-11 210280
sample-1 173988
sample-3 133036
sample-2 107743
sample-5 90754
sample-6 85523

After dad2 analysis

Sample ID Sequence Count
sample-9 114,019
sample-7 96,251
sample-11 82,305
sample-10 61,008
sample-3 57,312
sample-2 36,932
sample-5 32,659
sample-1 29,805
sample-12 2,747
sample-4 2,476
sample-8 2,463
sample-6 315

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.

A post was merged into an existing topic: Denoising results queries