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 name Sequence count
After dad2 analysis
(Zero implies no even sampling.)
Retained 518,292 (100.00%) sequences in 12 (100.00%) samples at the specifed sampling depth.
Number of SamplesSO_8154_S001_ITS1SO_8154_S001_ITS2SO_8154_S006_ITS1SO_8154_S006_ITS2SO_8154_S024_ITS1SO_8154_S024_ITS2SO_8154_S030_ITS1SO_8154_S030_ITS2SO_8154_S034_ITS1SO_8154_S034_ITS2SO_8154_S039_ITS1SO_8154_S039_ITS20.00.10.20.22.214.171.124.126.96.36.199
|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.