Commit bb2ae388 authored by Alessio Milanese's avatar Alessio Milanese
Browse files

Update README.md

parent 115d9ac0
......@@ -267,7 +267,7 @@ 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 -t 8
motus profile -f filtered_1P -r filtered_2P -s filtered_1U,filtered_2U -o test_sample.motus -t 8 -n test_sample
```
Which produces (`head test_sample.motus`):
......@@ -327,12 +327,12 @@ We use [mOTUs2](https://github.com/motu-tool/mOTUs_v2) to create taxonomic profi
If we run:
```
motus profile -f filtered_1P -r filtered_2P -s filtered_1U,filtered_2U -o test_sample_relax.motus -t 8 -g 1 -l 40
motus profile -f filtered_1P -r filtered_2P -s filtered_1U,filtered_2U -o test_sample_relax.motus -t 8 -g 1 -l 40 -n relax
cat test_sample_relax.motus | grep -v "0.0000000000" | grep -v "#" | wc -l
```
We obtain 356 species (198 more species than the default parameters). While, with:
```
motus profile -f filtered_1P -r filtered_2P -s filtered_1U,filtered_2U -o test_sample_stringent.motus -t 8 -g 6 -l 90
motus profile -f filtered_1P -r filtered_2P -s filtered_1U,filtered_2U -o test_sample_stringent.motus -t 8 -g 6 -l 90 -n stringent
cat test_sample_stringent.motus | grep -v "0.0000000000" | grep -v "#" | wc -l
```
we profile only 91 species (67 less than using the standard parameters).
......@@ -347,12 +347,7 @@ We use [mOTUs2](https://github.com/motu-tool/mOTUs_v2) to create taxonomic profi
4. How can you merge different motus profiles into one file?
Download the following profiles and merge them into one file.
```
wget https://www.embl.de/download/zeller/metaG_course/motus_profiles/tax_profiles.tar.gz
tar -zxvf tax_profiles.tar.gz
```
How the merged file differs from the example above?
Try to merge the three files created in the previous exercises into one profile.
<details><summary>SOLUTION</summary>
<p>
......@@ -362,22 +357,28 @@ We use [mOTUs2](https://github.com/motu-tool/mOTUs_v2) to create taxonomic profi
You can run:
```
motus merge -d tax_profiles -o all_samples.motus
motus merge -i test_sample.motus,test_sample_relax.motus,test_sample_stringent.motus -o all_samples.motus
```
which looks like (`head all_samples.motus`):
```
# motus version 2.5.1 | merge 2.5.1 | info merged profiles: # 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 /Users/milanese/Dropbox/PhD/mOTUsv2_tool/2.5.1/mOTUs_v2/motus merge -d tax_profiles -o all_samples.motus
#consensus_taxonomy VF_264 VF_47 VF_77 VF_90
Leptospira alexanderi [ref_mOTU_v25_00001] 0.0000000000 0.0000000000 0.0000000000 0.0000000000
Leptospira weilii [ref_mOTU_v25_00002] 0.0000000000 0.0000000000 0.0000000000 0.0000000000
Chryseobacterium sp. [ref_mOTU_v25_00004] 0.0000000000 0.0000000000 0.0000000000 0.0000000000
Chryseobacterium gallinarum [ref_mOTU_v25_00005] 0.0000000000 0.0000000000 0.0000000000 0.0000000000
Chryseobacterium indologenes [ref_mOTU_v25_00006] 0.0000000000 0.0000000000 0.0000000000 0.0000000000
Chryseobacterium artocarpi/ureilyticum [ref_mOTU_v25_00007] 0.0000000000 0.0000000000 0.0000000000 0.0000000000
Chryseobacterium jejuense [ref_mOTU_v25_00008] 0.0000000000 0.0000000000 0.0000000000 0.0000000000
# motus version 3.0.0 | merge 3.0.0 | info merged profiles: # git tag version 3.0.1 | motus version 3.0.1 | map_tax 3.0.1 | gene database: nr3.0.1 | calc_mgc 3.0.1 -y insert.scaled_counts -l 40 | calc_motu 3.0.1 -k mOTU -C no_CAMI -g 1 | taxonomy: ref_mOTU_3.0.1 meta_mOTU_3.0.1 # git tag version 3.0.1 | motus version 3.0.1 | map_tax 3.0.1 | gene database: nr3.0.1 | calc_mgc 3.0.1 -y insert.scaled_counts -l 75 | calc_motu 3.0.1 -k mOTU -C no_CAMI -g 3 | taxonomy: ref_mOTU_3.0.1 meta_mOTU_3.0.1 # git tag version 3.0.1 | motus version 3.0.1 | map_tax 3.0.1 | gene database: nr3.0.1 | calc_mgc 3.0.1 -y insert.scaled_counts -l 90 | calc_motu 3.0.1 -k mOTU -C no_CAMI -g 6 | taxonomy: ref_mOTU_3.0.1 meta_mOTU_3.0.1
# call: python motus merge -i test_sample.motus,test_sample_relax.motus,test_sample_stringent.motus -o all_samples.motus
#consensus_taxonomy test_sample relax stringent
Leptospira alexanderi [ref_mOTU_v3_00001] 0.0000000000 0.0000000000 0.0000000000
Leptospira weilii [ref_mOTU_v3_00002] 0.0000000000 0.0000000000 0.0000000000
Chryseobacterium sp. [ref_mOTU_v3_00004] 0.0000000000 0.0000000000 0.0000000000
Chryseobacterium gallinarum [ref_mOTU_v3_00005] 0.0000000000 0.0000000000 0.0000000000
Chryseobacterium indologenes [ref_mOTU_v3_00006] 0.0000000000 0.0000000000 0.0000000000
Chryseobacterium artocarpi/ureilyticum [ref_mOTU_v3_00007] 0.0000000000 0.0000000000 0.0000000000
Chryseobacterium jejuense [ref_mOTU_v3_00008] 0.0000000000 0.0000000000 0.0000000000
```
We can also check the one that are all different from zero by running:
```
cat all_samples.motus | grep -vP "0.0000000000\t0.0000000000\t0.0000000000"
```
Note that that if you want to load this table into another tool (for example R), you would like to skip the first 2 rows.
</p>
......
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