Hi,
I would like to get a table with each feature id and the frequency it occurs in each sample. in qiime I was unable to classify any of the features (they come back almost 100% unassigned in my taxa barplot)
index | Unassigned;;;;;; | d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Chloroplast;f__Chloroplast;g__Chloroplast;s__uncultured_bacterium | d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rickettsiales;f__Mitochondria;g__Mitochondria;s__Saccharina_japonica | d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Oceanospirillales;f__Marinomonadaceae;g__Marinomonas;s__uncultured_marine | Sequences | Strain | Culture_ID | Date | Site | culture | barplot_ID |
---|---|---|---|---|---|---|---|---|---|---|---|
1-18s | 64672 | 0 | 0 | 0 | 1-18S_R1_001.fastq.gz,1-18S_R2_001.fastq.gz | QT003 | 2_L_Flask_stage | 1/24/22 | Common garden | 2_L_Flask_stage | 2_L_Flask_stage 1/24/2022 |
10-18s | 70964 | 0 | 0 | 0 | 10-18S_R1_001.fastq.gz,10-18S_R2_001.fastq.gz | QT005 | Pre-split_pond_C3 | 3/1/22 | Common garden | CommonGarden_Pre-split_pond_QT005 | CommonGarden_Pre-split_pond_QT005 3/1/2022 |
11-18s | 60600 | 0 | 0 | 0 | 11-18S_R1_001.fastq.gz,11-18S_R2_001.fastq.gz | QT002 | Pre-split_pond_C4 | 3/1/22 | Common garden | CommonGarden_Pre-split_pond_QT002 | CommonGarden_Pre-split_pond_QT002 3/1/2022 |
but I have blasted each sequence and gotten results, so I would not like to tie those results to abundance. when I run
qiime feature-table summarize
--i-table uchime-dn-out-18s-trunc/table-nonchimeric.qza
--o-visualization uchime-dn-out-18s-trunc/table-nonchimeric-18s.qzv
I just get a visualization that shows me frequency per sample, but looks like this:
24-18s,171178.0
45-18s,127611.0
41-18s,115359.0
27-18s,114990.0
6-18s,114820.0
61-18s,112832.0
5-18s,98294.0
not quite what I'm looking for. I can also get:
Frequency | # of Samples Observed In | |
---|---|---|
f8bd3eed5b215a0bd7d09fd5f5ce26e6 | 168,828 | 1 |
dbe8f0eac8b7970b6b082145eb7167d3 | 124,751 | 1 |
bcf19f8c7828812fd03aa7fd575770ec | 113,814 | 2 |
which has the feature id and frequency in all the samples, but I need frequency PER sample.
I basically want the exact csv output I would get from taxa barplot but with just feature id and abundance. It doesn't help me to just see 'unassigned' and have all those features lumped together.
I hope this makes sense.
Thanks,
Stephanie