Commit 92e92123 authored by peguerin's avatar peguerin
Browse files

Update README.md

parent ca62f198
...@@ -118,25 +118,25 @@ verbose as possible — e.g. include the command line, etc ...@@ -118,25 +118,25 @@ verbose as possible — e.g. include the command line, etc
# 5. Running the pipeline # 5. Running the pipeline
## 5.1 Filter raw data ## 5.1 Filter raw data
`bash ./00-scripts/step1/filter_raw_data.sh` * `bash ./00-scripts/step1/filter_raw_data.sh`
## 5.2 Georeferenced sequences alignments by species ## 5.2 Georeferenced sequences alignments by species
`bash ./00-scripts/step2/seq_alnt_filtered_data.sh ` * `bash ./00-scripts/step2/seq_alnt_filtered_data.sh `
`mkdir ./06-species_alnt_cluster/total` * `mkdir ./06-species_alnt_cluster/total`
`mkdir ./06-species_alnt_cluster/freshwater` * `mkdir ./06-species_alnt_cluster/freshwater`
`mkdir ./06-species_alnt_cluster/marine` * `mkdir ./06-species_alnt_cluster/marine`
`bash ./00-scripts/step2/cluster_freshwater_vs_marine.sh` * `bash ./00-scripts/step2/cluster_freshwater_vs_marine.sh`
`Rscript ./00-scripts/step2/equalareacoords.R` * `Rscript ./00-scripts/step2/equalareacoords.R`
## 5.3 Species sequence pairwise comparison ## 5.3 Species sequence pairwise comparison
`julia ./00-scripts/step3/master_matrices.jl` * `julia ./00-scripts/step3/master_matrices.jl`
## 5.4 Genetic Diversity calculation ## 5.4 Genetic Diversity calculation
`julia ./00-scripts/step4/equalarea_numbers.jl` * `julia ./00-scripts/step4/equalarea_numbers.jl`
`bash ./00-scripts/step4/gdval_by_site.sh` * `bash ./00-scripts/step4/gdval_by_site.sh`
`julia ./00-scripts/step4/metrics_by_area_and_species.jl` * `julia ./00-scripts/step4/metrics_by_area_and_species.jl`
## 5.5 Statistical analysis ## 5.5 Statistical analysis
`Rscript ./00-scripts/step5/model_area_GDval.R` * `Rscript ./00-scripts/step5/model_area_GDval.R`
`Rscript ./00-scripts/step5/model_species-area_GDval.R` * `Rscript ./00-scripts/step5/model_species-area_GDval.R`
Supports Markdown
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment