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.