Update README.md

tax_practical/README.md

@@ -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>