Profile one sample

The mOTUs profiler takes as input one or multiple fastq files. The input can be zipped in .gz or .bz2 format. The output is a file with the relative abundance (or read counts) of the prokaryotic species found in the sample.

To profile samples we will use the command profile, type motus profile for the list of parameters.

Specify fastq input files

As fastq input is possible to provide paired end reads:

motus profile -f forward_reads.fastq -r reverse_reads.fastq

as well as single reads that comes from quality filtering:

motus profile -f forward_reads.fq -r reverse_reads.fq -s single_reads.fq

or only single reads if the sequencing was not performed with paired end reads:

motus profile -s single_reads.fq

Moreover, if the sample was divided in two (or more) lanes, is possible to profile all reads together:

motus profile -f for_r_lane1.fq,for_r_lane2.fq -r rev_r_lane1.fq,rev_r_lane2.fq

Specify the name of the sample

You can specify the name of the sample with the -n option. Example:

motus profile -s ERS199259_filetered.fq.gz -n ERS199259

In the resulting profile, the third header will be:

#consensus_taxonomy	ERS199259

If you do not specify the name, then the third header will be:

#consensus_taxonomy	unnamed sample

Note that the name that is specified with -n will be used in the merge function of motus.

If you do not specify the names, and merge samples, then it will not be possible to understand which column correspond to which sample. Example:

motus profile -s ERS199259_filetered.fq.gz -o ERS199259.motus
motus profile -s SRS190579_filetered.fq.gz -o SRS190579.motus

motus merge -i ERS199259.motus,SRS190579.motus

  #consensus_taxonomy                       unnamed sample    unnamed sample
  Kandleria vitulina [ref_mOTU_v2_0001]                 93                42
  Methyloversatilis universalis [ref_mOTU_v2_0002]       0                 4

Number of threads

You can specify the number of threads that you want to use with the -t option. Example:

motus profile -s ERS199259_filetered.fq.gz -t 4

We suggest to use 4 or 8 threads, note that the time needed for profiling is not scaling linearly with the number of threads.