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tax_practical/README.md

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 # Practical 2: Demonstration of mOTUs for taxonomic profiling
 
 Objectives of the practical:
@@ -271,15 +293,15 @@ We use [mOTUs2](https://github.com/motu-tool/mOTUs_v2) to create taxonomic profi
 
    We can have a look at the identified species that are different from zero with `cat test_sample.motus | grep -v "0.0000000000"`:
    ```
-   # 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 profile -f filtered_1P -r filtered_2P -s filtered_1U,filtered_2U -o test_sample.motus -t 2
+   # 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
-   Proteobacteria sp. [ref_mOTU_v25_00095]	0.0001743716
-   Eggerthella lenta [ref_mOTU_v25_00719]	0.0001584466
-   Ruminococcus bromii [ref_mOTU_v25_00853]	0.0040007632
+   Escherichia coli [ref_mOTU_v3_00095]	0.0001797485
+   Eggerthella lenta [ref_mOTU_v3_00719]	0.0001633324
+   Ruminococcus bromii [ref_mOTU_v3_00853]	0.0049443856
    ```
    
-   With `cat test_sample.motus | grep -v "0.0000000000" | grep -v "#" | wc -l`, we can see that we have 139 detected species.
+   With `cat test_sample.motus | grep -v "0.0000000000" | grep -v "#" | wc -l`, we can see that we have 158 detected species.
    
    To count the number of ref-mOTUs you can use:
    ```
@@ -289,6 +311,10 @@ We use [mOTUs2](https://github.com/motu-tool/mOTUs_v2) to create taxonomic profi
    ```
    cat test_sample.motus | grep -v "0.0000000000" | grep -c "meta_mOTU_"
    ```
+   and for meta-mOTUs:
+   ```
+   cat test_sample.motus | grep -v "0.0000000000" | grep -c "ext_mOTU_"
+   ```
    </p>