Commit 3c5b0c9a authored by Alessio Milanese's avatar Alessio Milanese
Browse files

Update to motus 3

parent bd4bcd4e
......@@ -245,24 +245,24 @@ We use [mOTUs2](https://github.com/motu-tool/mOTUs_v2) to create taxonomic profi
You can profile the sample with:
```
motus profile -f filtered_1P -r filtered_2P -s filtered_1U,filtered_2U -o test_sample.motus
motus profile -f filtered_1P -r filtered_2P -s filtered_1U,filtered_2U -o test_sample.motus -t 8
```
Which produces (`head test_sample.motus`):
```
# git tag version 2.5.1 | motus version 2.5.1 | map_tax 2.5.1 | gene database: nr2.5.1 | calc_mgc 2.5.1 -y insert.scaled_counts -l 75 | calc_motu 2.5.1 -k mOTU -C no_CAMI -g 3 | taxonomy: ref_mOTU_2.5.1 meta_mOTU_2.5.1
# call: python motus profile -f filtered_1P -r filtered_2P -s filtered_1U,filtered_2U -o test_sample.motus
#consensus_taxonomy unnamed sample
Leptospira alexanderi [ref_mOTU_v25_00001] 0.0000000000
Leptospira weilii [ref_mOTU_v25_00002] 0.0000000000
Chryseobacterium sp. [ref_mOTU_v25_00004] 0.0000000000
Chryseobacterium gallinarum [ref_mOTU_v25_00005] 0.0000000000
Chryseobacterium indologenes [ref_mOTU_v25_00006] 0.0000000000
Chryseobacterium artocarpi/ureilyticum [ref_mOTU_v25_00007] 0.0000000000
Chryseobacterium jejuense [ref_mOTU_v25_00008] 0.0000000000
```
In the profile, `ref_mOTU` represent species with a reference genome sequence in NCBI. While `meta_mOTU` represent species that have not been sequenced yet (they do not have a representative genome in NCBI).
the `-1` at the end of the file (check with `tail test_sample.motus`), represents species that we know to be present, but are not able to profile. The `-1` is useful to have a correct evaluation of the relative abundance of all species (more info [here](https://github.com/motu-tool/mOTUs_v2/wiki/Explain-the-resulting-profile#-1)).
# git tag version 3.0.0 | motus version 3.0.0 | map_tax 3.0.0 | gene database: nr3.0.0 | calc_mgc 3.0.0 -y insert.scaled_counts -l 75 | calc_motu 3.0.0 -k mOTU -C no_CAMI -g 3 | taxonomy: ref_mOTU_3.0.0 meta_mOTU_3.0.0
# call: python /g/scb2/zeller/milanese/motus_v2/update_DB/mOTUs/motus profile -f filtered_1P -r filtered_2P -s filtered_1U,filtered_2U -o test_sample.motus -t 16
#consensus_taxonomy unnamed sample
Leptospira alexanderi [ref_mOTU_v3_00001] 0.0000000000
Leptospira weilii [ref_mOTU_v3_00002] 0.0000000000
Chryseobacterium sp. [ref_mOTU_v3_00004] 0.0000000000
Chryseobacterium gallinarum [ref_mOTU_v3_00005] 0.0000000000
Chryseobacterium indologenes [ref_mOTU_v3_00006] 0.0000000000
Chryseobacterium artocarpi/ureilyticum [ref_mOTU_v3_00007] 0.0000000000
Chryseobacterium jejuense [ref_mOTU_v3_00008] 0.0000000000
```
In the profile, `ref_mOTU` represent species with a reference genome sequence in NCBI. While `meta_mOTU` and `ext_mOTU` represent species that have not been sequenced yet (they do not have a representative genome in NCBI).
the `unassigned` at the end of the file (check with `tail test_sample.motus`), represents species that we know to be present, but are not able to profile. The `unassigned` is useful to have a correct evaluation of the relative abundance of all species (more info [here](https://github.com/motu-tool/mOTUs_v2/wiki/Explain-the-resulting-profile#-1)).
</p>
2. How many species are detected? How many are reference species and how many are unknown species?
......
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