Merge profiles into a table

Once you profiled all your samples, you can merge them in a unique file (a tab separated matrix).

There are two ways to merge profiles:

• providing a list of files
• merging all files contained in a directory

Provide a list of files

You can merge files providing a comma separated list of files. Example with three files:

$ ls
sample_34.motus
sample_XY.motus
sampZ.motus

You can merge them with:

motus merge -i sample_34.motus,sample_XY.motus,sampZ.motus

Merge all files contained in a directory

If you save all your profile files in a directory, example:

$ ls results/
sample_34.motus
sample_XY.motus
sampZ.motus

You can merge all files contained in the directory with the -d option:

motus merge -d results

You can specify the output file with -o. The merged file looks like:

# motus version 2.1.0 | merge 2.1.0 | info merged profiles: # git tag version 2.0.0 |  motus version 2.0.0 | map_tax 2.0.0 | gene database: nr2.0.0 | calc_mgc 2.0.0 -y insert.raw_counts -l 75 | calc_motu 2.0.0 -k mOTU -g 3 -c | taxonomy: ref_mOTU_2.0.0 meta_mOTU_2.0.0 
# call: python mOTUs_v2/motus merge -i test/test1.motus,test/test2.motus
#consensus_taxonomy	sample1	sample2
Kandleria vitulina [ref_mOTU_v2_0001]	93	42
Methyloversatilis universalis [ref_mOTU_v2_0002]	0	0
Megasphaera genomosp. [ref_mOTU_v2_0003]	11	3
Streptococcus anginosus [ref_mOTU_v2_0004]	22	298
Streptococcus anginosus [ref_mOTU_v2_0005]	0	0

Note that the name of the samples is in the third header (#consensus_taxonomy sample1 sample2). You need to specify the name of the samples when profiling with the -n option. For example:

motus profile -s test1.fq -n sample1 -o test1.motus