Commit ea31b059 authored by Alessio Milanese's avatar Alessio Milanese
Browse files

update to motus 3.0.1

parent d7e4faca
......@@ -272,8 +272,8 @@ We use [mOTUs2](https://github.com/motu-tool/mOTUs_v2) to create taxonomic profi
Which produces (`head test_sample.motus`):
```
# 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
# 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
# call: python /nile/DB/milanese/CONDA/miniconda3.9/bin/../share/motus-3.0.1//motus profile -f filtered_1P -r filtered_2P -s filtered_1U,filtered_2U -o test_sample.motus -t 8
#consensus_taxonomy unnamed sample
Leptospira alexanderi [ref_mOTU_v3_00001] 0.0000000000
Leptospira weilii [ref_mOTU_v3_00002] 0.0000000000
......@@ -293,8 +293,8 @@ 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 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
# 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
# call: python /nile/DB/milanese/CONDA/miniconda3.9/bin/../share/motus-3.0.1//motus profile -f filtered_1P -r filtered_2P -s filtered_1U,filtered_2U -o test_sample.motus -t 8
#consensus_taxonomy unnamed sample
Escherichia coli [ref_mOTU_v3_00095] 0.0001797485
Eggerthella lenta [ref_mOTU_v3_00719] 0.0001633324
......@@ -327,11 +327,11 @@ 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 2 -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
cat test_sample_relax.motus | grep -v "0.0000000000" | grep -v "#" | wc -l
```
We obtain 218 species (79 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 2 -g 6 -l 90
cat test_sample_stringent.motus | grep -v "0.0000000000" | grep -v "#" | wc -l
```
......
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