Commit d7e4faca authored by Alessio Milanese's avatar Alessio Milanese
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Update README.md

parent 848f312d
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# Practical 2: Demonstration of mOTUs for taxonomic profiling
Objectives of the practical:
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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:
```
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```
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>
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