Hello. Created a feature table using qiime2/dada2 and it looks weird. The ASVs with the highest counts are at the top of the table and the table gets progressively sparse with fast scrolling; a relatively short gradient.
Additionally, I noticed several ASVs that contain zeros for all but 1 of 38 samples contain a strange pseudo count that counts. The number counts down from 20-something, is never in the same sample for all ASVS, and is staggered in such a way as to make a diagonal line.
Below is my series of keystrokes:
1. activate qiime 2 environment: source activate qiime2-2020.6
2. Created the maifest file: SMP_ASVmanifest.csv
3. Imported the manifest file
nohup qiime tools import --type 'SampleData[PairedEndSequencesWithQuality]' --input-path SMP_ASVmanifest.csv --output-path demux-2018_2019 --input-format PairedEndFastqManifestPhred33 > nohup.out 2> nohup.err &
4. Next step is to look at the quality plot, make trimming decisions and do two DADA2 trial runs.
5. form the ASVs using DADA2
nohup qiime dada2 denoise-paired --i-demultiplexed-seqs demux-2018_2019.qza --p-n-threads 15 --p-trim-left-f 20 --p-trim-left-r 20 --p-trunc-len-f 250 --p-trunc-len-r 227 --o-table table-2018_2019-nc.qza --o-representative-sequences repseqs-2018_2019-nc.qza --o-denoising-stats stats-2018_2019-nc.qza
6. Apply taxonomy to the non cutadapted repseqs
nohup qiime feature-classifier classify-sklearn --i-classifier /usr/local/bioinf/tax_db/Pr2_V12_Qiime2-2020.6/Pr2_Classifier_V12_Q2-2020.qza --p-n-jobs 15 --i-reads repseqs-2018_2019-nc.qza --o-classification taxonomy-2018_2019
7. export the table
qiime tools export --input-path table-2018_2019-nc.qza --output-path exported-table-2018_2019&
biom convert -i exported-table-2018_2019/feature-table.biom -o feature_table-2018_2019.txt --to-tsv --header-key=taxonomy
8. export the representative sequences
qiime tools export --input-path repseqs-2018_2019-nc.qza --output-path exported-repseqs-2018_2019
Toy example of pattern below (more samples and ASVs involved on actual table):
Sample1 Sample2 Sample3 Sample4 Sample 5
ASV_1 24 0 0 0 0
ASV_2 0 24 0 0 0
ASV_3 0 0 24 0 0
ASV_4 0 0 0 0 0
ASV_5 23 0 0 0 0
ASV_6 0 23 0 0 0
ASV_7. 0 0 23 0 0
I've attached the feature table exported from qiime2 and highlighted the patterns in excel. Pattern starts (mildly) at line 3015 counting down from the number 15. More extreme cases are in the single digits around line 4373 (the number "8").
I can share any other data, tables, screenshots as needed.
Please help shine some light on what's going on.
Thanks,feature_table-2018_2019.txt (7.5 MB)
Gerid