2269 feature-table.tsv
2269 taxonomy.tsv
There are two head lines in feature-table.tsv while there is only one head line in taxonomy.tsv, so the sequence numbers are not equal.
This is a robust method, that uses the source Artifacts and counts the feature IDs:
# transpose feature table to get features as primary axis
qiime feature-table transpose \
--i-table table.qza \
--o-transposed-feature-table transposed-table.qza
qiime tools inspect-metadata transposed-table.qza | grep ID | awk '{ print $2 }'
qiime tools inspect-metadata taxonomy.qza | grep ID | awk '{ print $2 }'
When you run these you should get a number for each inspect-metadata command (2), which should match. For example, using moving pictures tutorial, I see 770 as the result for both.
Hi, @thermokarst, thanks for your reply!!!
I used ‘qiime tools export’ and ‘biom convert’ to get the ‘taxonomy.tsv’ and ‘feature-table.tsv’(from the table.qza) and then used the linux ‘wc -l’ to count the lines.
Yes, I used the methods you provided and the number is the same.
When I unzip the table.qza to feature-table.tsv, there are two lines:
Constructed from biom file
#OTU ID S1 S2 S3 S4 S5
Although the number of lies of feature-table.tsv is the same as taxonomy.tsv, but I check the all the seq id in feature-table.tsv can be found in taxonomy.tsv. So I guess the last line of feature-table.tsv might lack of ‘\n’ and it was not counted by ‘wc -l’.
@thermokarst, hello, Could you tell me how to add taxonomic infos to the table.qza?
I followed your methods as described before, but it did not work out.
Thanks!
thermokarst
(Matthew Ryan Dillon)
assigned thermokarst
#5
Did you follow all of the steps? Are you sure you are looking at the right data files? That protocol has been verified many times --- please double check your workflow.
thermokarst
(Matthew Ryan Dillon)
unassigned thermokarst
#7