Hello fellow qiime2 users,
I've been trying to figure out differentially abundant microbial population in diabetic patients but facing so many obstacles that I can't figure out alone as a novice metagenomic analyst, so I need your help and I'm attaching all the files I used and errors I got below. For the analysis, I merged my feature and metadata tables, filtered out mitochondrial and chloroplast sequence and now trying to use the final FeatureTable [Frequency] for the qiime composition ancombc to generate a barplot. And somehow I was successful before using the following code:
qiime composition ancombc
qiime composition da-barplot
final_filtered_table(old).qza (3.1 MB)
DA_diffbar.qzv (850.4 KB)
differentials.qza (736.5 KB)
metadata_final.tsv (708.0 KB)
However, the barplot that I prepared didn't have taxa name and was too large for any good use. so I was trying to resolve how to get past that. I collapsed my table down to phylum and genus level but the tables were now in FeatureTable [composition] format so they couln't be used in the plugin/code I used before.
merged_table_genus.qza (673.9 KB)
merged_table_phylum.qza (372.5 KB)
However, now that I'm trying to run the same code I ran before (after a while), I'm 'getting errors no matter what file I use, filtered or unfiltered feature tables also with different metadata.
I've also tried using other codes that I saw in the forum, such as:
filtered_combo_table.qza (3.1 MB)
combined_deblur_table.qza (2.9 MB)
qiime ancombc ancombc --i-table filtered_combo_table.qza --m-metadata-file metadata_final.tsv --p-formula "Diabetes_typ" --o-differentials da_test.qza --verbose
And also checked conda list as one post asks, and found something unusual maybe:
With my deadlines approaching I'm a bit lost so I'd be very grateful if someone could help me solve this mess. I searched for a proper step-by-step tutorial for the analysis but couln't find it anywhere on the documentation or forum, so proper documentation or tutorial would also help.
Thanks in Advance.
I updated my qiime2 environment and was able to resolve the whole error above by using collapsed table for DA test, however,
DA_gen.qzv (720.1 KB)
there were too many samples to I tried filtering the table using the following code:
qiime feature-table filter-features-conditionally
and then collapsed this table:
qiime taxa collapse
However now that I'm trying to use this table, there's another error-
I tried to check documentation and added parameter to filter missing value if there was any,
qiime composition ancombc
but the parameter wasn't accepted for some reason.
Can someone help me with how to shorten the list of features, or why my filtered table isn't working?
This looks like you filtered all the samples out. Can you summarize col_tab_genus_30.qza and see if it is empty like I am hypothesizing
Yes, you're absolutely correct.
Does that mean I don't have any samples with a minimum 30% prevalence?
However when I run this code instead, with manually computed 30% number of my samples it does show a viable feature table.
qiime feature-table filter-features \
--i-table filtered_combo_table.qza \
--p-min-samples 204 \
--p-min-frequency 50 \
qiime feature-table summarize \
--i-table col_tab_genus_30_freq50.qza \
--m-sample-metadata-file metadata_final.tsv \
Pardon my lack of knowledge, Could you kindly point out the differences here?
I would think that that means that you dont have any features (ASVs/OTUs) that are present in 30% or more of your samples/you dont have any features that are above 1% abundance.
I would try re-running this command
without the --p-abundance parameter. Lets see if that result is more similar to your manual attempt at filtering to 30% prevalence.
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