Commit 60be623a authored by Alessio Milanese's avatar Alessio Milanese
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Update README.md

parent bb2ae388
......@@ -389,22 +389,25 @@ We use [mOTUs2](https://github.com/motu-tool/mOTUs_v2) to create taxonomic profi
We can profile the unfiltered reads with:
```
motus profile -f raw_reads_1.fastq -r raw_reads_2.fastq -t 2 -n unfiltered -o unfiltered.motus
motus profile -f raw_reads_1.fastq -r raw_reads_2.fastq -t 8 -n unfiltered -o unfiltered.motus
```
Let's have a look at the species that are profiled by both:
```
motus merge -i unfiltered.motus,test_sample.motus | grep -v "0.0000000000" | grep -v "#"
motus merge -i unfiltered.motus,test_sample.motus | grep -v "0.0000000000" | grep -v "#" | head
```
Which results in:
```
Proteobacteria sp. [ref_mOTU_v25_00095] 0.0002007051 0.0001743716
Eggerthella lenta [ref_mOTU_v25_00719] 0.0001496362 0.0001584466
Ruminococcus bromii [ref_mOTU_v25_00853] 0.0037746076 0.0040007632
Bacteroides rodentium/uniformis [ref_mOTU_v25_00855] 0.0212321086 0.0214878111
Anaerostipes hadrus [ref_mOTU_v25_00857] 0.0001321414 0.0001399217
Roseburia faecis [ref_mOTU_v25_00859] 0.0003954637 0.0004187479
Roseburia inulinivorans [ref_mOTU_v25_00860] 0.0001544263 0.0001639940
Escherichia coli [ref_mOTU_v3_00095] 0.0002054152 0.0001797485
Eggerthella lenta [ref_mOTU_v3_00719] 0.0001531478 0.0001633324
Ruminococcus bromii [ref_mOTU_v3_00853] 0.0046285150 0.0049443856
Bacteroides uniformis [ref_mOTU_v3_00855] 0.0179185757 0.0188356677
Anaerostipes hadrus [ref_mOTU_v3_00857] 0.0000810850 0.0000864773
Roseburia faecis [ref_mOTU_v3_00859] 0.0003944823 0.0004207160
Roseburia inulinivorans [ref_mOTU_v3_00860] 0.0001580503 0.0001690509
Roseburia hominis [ref_mOTU_v3_00861] 0.0004800660 0.0005119912
Bifidobacterium longum [ref_mOTU_v3_01099] 0.0023339573 0.0027482230
Megasphaera elsdenii [ref_mOTU_v3_01516] 0.0006391750 0.0006816812
```
The two profiles are really similar. mOTUs is filtering the reads internally based on how good they map to the marker gene sequences; hence trimming and filtering the reads before will not affect much the profiles. For other analysis (like building metagenome-assembled genomes) trimming the reads improve the result.
......
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