Phylogenetic Tree Construction with Fasttree

Marian Schmidt

July 3rd, 2018

For All OTUs that pass the RL score threshold: 258 OTUs

1. Create this repo in the fasttree folder.

2. To plot a phylogeny with OTUs with HNA and LNA Lasso Scores to look for phylogenetic signal. The following code was ran in R with the vector of OTUs with RL scores of at least 0.15:

# With all of the OTUs that pass the RL score threshold
otu_scores_df <- matrix_RLscores %>%
  as.data.frame() %>%
  tibble::rownames_to_column("OTU")

# Subset the vector with names of the OTUs
vector_of_otus <- as.vector(otu_scores_df$OTU)

# Write a file 
write(vector_of_otus, file = "data/fasttree/Figure5/OTUnames_RLscores_258.txt",
      ncolumns = 1, append = FALSE, sep = "\n")

1. Next, I ran the following code in the shell:

~/bbmap/filterbyname.sh in=../cut_test.fasta names=OTUnames_RLscores_258.txt out=OTUs258.fasta -include t

1. Since the above function puts an “N” where all the dashes are for alignment - let’s replace them with “-“ by running the following command.

sed 's/N/-/g' OTUs258.fasta > OTUs258_rmN.fasta

For the Top 10 OTUs from each system: 41 OTUs

1. Make file with OTU names in R:

# Get the Top 10 OTU names
top10_otu_scores_df <- df_top10 %>%
  as.data.frame() 

# Subset the vector with names of the OTUs
top10_vector_of_otus <- as.vector(top10_otu_scores_df$OTU)

# Write the file 
write(top10_vector_of_otus, file = "data/fasttree/Figure5/OTUnames_RLscores_top10.txt",
      ncolumns = 1, append = FALSE, sep = "\n")

1. Subset the sequences from the top 10 OTUs from the larger fasta file with filterbyname.sh from bbtools.

NOTE: If a file already exists - the command will not run because of overwrite=FALSE

~/bbmap/filterbyname.sh in=../cut_test.fasta names=OTUnames_RLscores_top10.txt out=OTUs_top10.fasta -include t

1. Remove the N’s for -.

sed 's/N/-/g' OTUs_top10.fasta > OTUs_top10_rmN.fasta

Copy Files to flux

1. I will use the transfer host through U of M (requires password). Working on my own personal computer in /scratch/lsa_fluxm/marschmi/HNA_LNA/June_July_2018.

# All 258 RLscore threshold OTUs
scp OTUs258_rmN.fasta flux-xfer.arc-ts.umich.edu:/scratch/lsa_fluxm/marschmi/HNA_LNA/June_July_2018

# Top 10 OTUs from each syste
scp OTUs_top10_rmN.fasta flux-xfer.arc-ts.umich.edu:/scratch/lsa_fluxm/marschmi/HNA_LNA/June_July_2018

Run FastTree

1. Run the fasttree pbs scripts with qsub fasttree_top10.pbs and qsub fasttree_OTUs_258.pbs.

2. After running fasttree, transfer those files back local computer. I ran code like (password required):

scp flux-xfer.arc-ts.umich.edu:/scratch/lsa_fluxm/marschmi/HNA_LNA/June_July_2018/FastTree* .
scp flux-xfer.arc-ts.umich.edu:/scratch/lsa_fluxm/marschmi/HNA_LNA/June_July_2018/newick* .