I am filtering my feature-table by featureid. I want to keep the featureid included in my tsv file "unmapped_reads" which is a tsv file, with only one column with the featureids in each row (6077 feature ids) and a header (first row) which is 'featureid'.
My orignal table, which I want to filter has 13049 features. In my filtered table I want to have only the 6077 features that I have in my tsv file.
The comands that I have used is below (when I tried to keep my wanted features, 6077 in total):
or this other one (when I tried to exclude that features, 6077, keeping 6972 in total):
qiime feature-table filter-features --i-table Table_dada2pyro_Original.qza --m-metadata-file unmapped_reads.tsv --p-exclude-ids --o-filtered-table FilteredTable_dada2pyro.qza
In both cases my filtered table has had 3561 features which is obviously an error. I do not know why this number and why in both cases independantly I am excluding or keeping my wanted features.
Do you know what is happening?
I am running qiime2-2021.4
Should I change my version? I use that one because is the version available in the external server that I am using.
To confirm, you're talking about the number of features (770 in the example below), and not the total frequency (153807 in the example below) of all observed features?
Sorry for dealying in my answer.
Yes, exactly. I am talking about number of features.
Regarding to send you the tables, how could I send them to you in a privet way? This data are unpublished so I prefer do not publish the tabñes in the forum. Is this possible?
Thanks for sharing your data, @MMC_northS. This action is behaving as expected - the reason you're seeing fewer features than you anticipated is simply because the action is filtering all empty samples/features out, too (because you haven't overridden the default for the --p-filter-empty-samples flag):
--p-filter-empty-samples / --p-no-filter-empty-samples
If true, drop any samples where none of the retained
features are present. [default: True]
If I disable that parameter I see 6,972, just as expected.
Thank you very much @thermokarst for your help! I really appreciate it
I did not realice that this option was activated by default. Sorry about my slip.
Thank you again!