FAQ#

How many mOTUs insert counts should I expect to have?#

In general, the number of mOTUs insert counts is generally proportional to the number of reads in the FastQ/A files, unless the environment is not well represented in the data used to build the mOTUs marker gene database.

Here is an overview of mOTUs counts expected at different sequencing depths based on human fecal samples:

Total number of reads (million)	Median mOTUs count
5	600
8	900
15	1,900
25	3,300
35	5,500
50	8,800
100	13,000

Why do only a few reads map in my profiles?#

One possibility is that all the reads have been filtered out. By default, motus profile filters out all the reads that map with less than 75 nucleotides (-l 75). If your reads are shorter on average (e.g., from older metagenomic samples), try decreasing the alignment length with the -l flag (see Alignment length in the option manual).

You can also try to increase recall by decreasing the number of marker genes required to detect a mOTU with the -g flag (see Number of marker genes in the option manual).

Another possibility is that the microbial community from your sample is not well represented by the genomes in the mOTUs marker gene database. This can happen if your sample originates from an understudied environment with limited shotgun metagenomic data available. You can find an overview of the environments used for MAG reconstruction on the mOTUs-db Samples page.

What is the meaning of mOTUv4.0_unassigned?#

The mOTUv4.0_unassigned at the end of the profile file represents the fraction of reads that mapped to marker genes not yet linked to a specific mOTU. This value represents the fraction of the microbial community that is known to be present but cannot be quantified at the species level.

You can include this value during calculate relative abundances or to perform rarefaction, but it’s better to remove this value from subsequent diversity or differential abundance analyses as it does not represent a single species.

To illustrate the benefit of calculating the unassigned fraction, let’s assume the following microbial community composition:

	True relative abundance
species 1	40%
species 2	5%
species 3	10%
species 4	30%
species 5	15%

If species 2 and species 5 are not represented in the mOTUs marker gene database, here is the taxonomic profile generated including the unassigned fraction:

	mOTUs read counts	mOTUs relative abundance
species 1	400	40%
species 3	100	10%
species 4	300	30%
unassigned	200	20%

And here is the taxonomic profile without the unassigned fraction, resulting in skewed relative abundances:

	mOTUs read counts	mOTUs relative abundance
species 1	400	50.0%
species 3	100	12.5%
species 4	300	37.5%

Where can I find the taxonomic annotation for each mOTU?#

You can find all files associated with the mOTUs marker gene database on Zenodo:

Alternatively, if you installed the mOTUs tool, the taxonomy files are available in the db_mOTU folder:

mOTUsv4.0.gtdb.taxonomy.80mv.tsv.gz: The taxonomic assignment for each mOTU based on an 80% majority vote across all genomes belonging to this mOTU. This is the taxonomy printed by default after running motus profile.
mOTUsv4.0.gtdb.taxonomy.rep.tsv.gz: The taxonomic assignment for each mOTU based on the taxonomic assignment of its representative genome.

I have profiles generated with mOTUs3. How can I compare these to mOTUs4 profiles?#

If possible, we recommend re-running mOTUs4 on your samples as the identifiers are directly compatible with mOTUs-db .

However, we prove a mapping file mOTUs3.1_2_mOTUs4.0.map.tsv.gz showing the correspondance between mOTUs3.1 and mOTUS4.0 cluster identifiers, which can be found amongst files associated with the mOTUs marker gene database on Zenodo:

Alternatively, if you installed the mOTUs tool, the file can be found in the db_mOTU folder.

How can I contact you if I have any questions?#

Please refer to the information provided on our About and contact page.

mOTUs is part of SIB's portfolio of open tools and databases.

mOTUs is part of the ELIXIR-CH Service Delivery Plan.