Closed xapple closed 1 year ago
Running Version: 2.5.1
Good Morning @xapple
We would encourage you to switch to a more recent version as 2.5 is based on data from 2019. Version 3 includes data from MAGs from 23 environments --> https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01410-z
The -1 (in version 3 it is called unassigned) represents the abundance of unknown species. This fraction is important to normalise e.g the relative the abundance within a sample but also to compare multiple samples with another (see Figure 2 in https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.218 and Figure 1 in the https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01410-z). So no, don't remove it.
Best, Hans
Thanks for your quick answer, and the explanation for the last time.
I will update the version to 3.1.0. For some reason when I typed conda install motus
that's the version I got. Probably because of a convoluted dependency exclusion graph in the current environement.
May I suggest to title the unassigned reads with unassigned
or unknown
instead of -1
in the output files.
I ran the following command, with some artificially simulated HiSeq paired-end reads:
And when I look at the output TSV file, the last line seems like a bug. Here is the tail of the file
motus.tsv
:Should we just deleted the last line in this case ? Is it safe to ignore ?