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 ...@@ -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: 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: 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: Which results in:
``` ```
Proteobacteria sp. [ref_mOTU_v25_00095] 0.0002007051 0.0001743716 Escherichia coli [ref_mOTU_v3_00095] 0.0002054152 0.0001797485
Eggerthella lenta [ref_mOTU_v25_00719] 0.0001496362 0.0001584466 Eggerthella lenta [ref_mOTU_v3_00719] 0.0001531478 0.0001633324
Ruminococcus bromii [ref_mOTU_v25_00853] 0.0037746076 0.0040007632 Ruminococcus bromii [ref_mOTU_v3_00853] 0.0046285150 0.0049443856
Bacteroides rodentium/uniformis [ref_mOTU_v25_00855] 0.0212321086 0.0214878111 Bacteroides uniformis [ref_mOTU_v3_00855] 0.0179185757 0.0188356677
Anaerostipes hadrus [ref_mOTU_v25_00857] 0.0001321414 0.0001399217 Anaerostipes hadrus [ref_mOTU_v3_00857] 0.0000810850 0.0000864773
Roseburia faecis [ref_mOTU_v25_00859] 0.0003954637 0.0004187479 Roseburia faecis [ref_mOTU_v3_00859] 0.0003944823 0.0004207160
Roseburia inulinivorans [ref_mOTU_v25_00860] 0.0001544263 0.0001639940 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. 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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