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Minimal Tutorial

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Jennifer Chang edited this page Nov 20, 2019 · 5 revisions

This is a draft and not live yet

This will be a step-by-step walk-through of running octoFLU on a sample fasta file.

Step 1: Download the Sample File

Download the sample_strains.fasta file from octo_demofiles

Step 2: Run octoFLU on the Sample File

bash pipeline.sh sample_strains.fasta

You should view a scrolling window similar to below:

Put gif of scrolling output here

Step 3: Take a look at the output folder

cd sample_strains.fasta_output
ls -ltr

# -rw-r--r--  1 username  macusers    50K Nov 20 15:35 blast_output.txt
# -rw-r--r--  1 username  macusers   269K Nov 20 15:35 H1_aln.fa
# -rw-r--r--  1 username  macusers    15K Nov 20 15:35 H1.tre
# -rw-r--r--  1 username  macusers   331K Nov 20 15:35 H3_aln.fa
# -rw-r--r--  1 username  macusers    19K Nov 20 15:36 H3.tre
# -rw-r--r--  1 username  macusers   137K Nov 20 15:36 N1_aln.fa
# -rw-r--r--  1 username  macusers   9.6K Nov 20 15:36 N1.tre
# -rw-r--r--  1 username  macusers   262K Nov 20 15:36 N2_aln.fa
# -rw-r--r--  1 username  macusers    17K Nov 20 15:36 N2.tre
# -rw-r--r--  1 username  macusers   346K Nov 20 15:36 PB2_aln.fa
# -rw-r--r--  1 username  macusers    14K Nov 20 15:36 PB2.tre
# -rw-r--r--  1 username  macusers   334K Nov 20 15:37 PB1_aln.fa
# -rw-r--r--  1 username  macusers    14K Nov 20 15:37 PB1.tre
# -rw-r--r--  1 username  macusers   361K Nov 20 15:37 PA_aln.fa
# -rw-r--r--  1 username  macusers    16K Nov 20 15:37 PA.tre
# -rw-r--r--  1 username  macusers   263K Nov 20 15:37 NP_aln.fa
# -rw-r--r--  1 username  macusers    16K Nov 20 15:37 NP.tre
# -rw-r--r--  1 username  macusers   192K Nov 20 15:37 M_aln.fa
# -rw-r--r--  1 username  macusers    17K Nov 20 15:37 M.tre
# -rw-r--r--  1 username  macusers   129K Nov 20 15:37 NS_aln.fa
# -rw-r--r--  1 username  macusers    13K Nov 20 15:38 NS.tre
# -rw-r--r--  1 username  macusers    20K Nov 20 15:38 sample_strains.fasta_Final_Output.txt
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