Understanding the representative sequence output

User Support
1

Hello,

I exported the representative sequences after demultiplexing and denoising the forward reads from Illumina sequencing using the following command:

###DENOISING
qiime dada2 denoise-single
--i-demultiplexed-seqs demux_C7.qza
--p-trim-left 80
--p-trunc-len 243
--p-n-threads 4
--o-table table_C7_trimmed.qza
--o-representative-sequences rep-seqs_C7_trimmed.qza
--o-denoising-stats denoising-stats_C7_trimmed.qza

###EXPORTING REPRESENTATIVE SEQUENCES IN FASTA FORMAT
qiime tools export
--input-path rep-seqs_C7_trimmed.qza
--output-path rep-seqs_C7_trimmed

###CHECKING THE TABLE SUMMARY
qiime feature-table summarize
--i-table table_C7_trimmed.qza
--o-visualization table_C7_trimmed_summary.qzv

The table summary output showed 235 unique features with a total sequence count of 33,167.

The top five features and their frequencies :
69e119b933b91f1a4516ee9c97269d7a → 21,043
e72522782cdd0fe08cac6328955837b6 → 2,577
c340786bb6e6d3d7633fb5e261a9f9b6 → 1,028
e8c4ffdd2a0dc53ee6dba1b2e4e57c8a → 728
52be977a8c3b47396520225710702754 → 391

Does this mean that all 21,043 sequences corresponding to 69e119b933b91f1a4516ee9c97269d7a are identical?

Look forward to receiving your insights.

Sincerely,

1 Like
2

Hello!
Yes, you are totally right!
ASVs, unlike OTUs, are unique sequences that you get after Dada2. All sequences, sharing the same sequence ID in Qiime2, are identical to each other.

Best,

2 Likes
3

Thank you very much for your quick response. Truly appreciate it.

Sincerely,

1 Like