Downloading Files Using Cyberduck Download the Centralia_Case_Study folder with all of your data to your Desktop instance using Cyberduck. Start Cyberduck. It is in your applications folder. Cyberduck allows you to transfer files between your computer and the Amazon EC2 instance you are running. Click on Connection” in the upper left of the window, and choose SFTP from the top drop-down menu. “Open Type the IP address for your EC2 instance (It is on the blackboard) into the Server window in Cyberduck. Type ubuntu (exactly as written!) as your username. You do not need a password. Click on Public Key Authentication’ at the bottom of the Cyberduck window and then migrate to and choose your ‘Use key pair (it should be on your desktop as QIIME-1.pem). Your Cyberduck window should now look something like the figure on the left. If it does, click on Then click on A new window will open up in Cyberduck when it has connected to “Connect”. ‘allow’. the server. To copy all of your Centralia files to your desktop, simply drag and drop your Centralia_Case_Study folder into the desktop of your computer. Say yes to replace the current folder. Copying these files may take a while, so go take a break if it does. Find your Centralia_Case_Study folder on your desktop and open it, and then open the rarification_plots folder. Double click on rarefication_plots.html to open it. You should see a browser window that looks like this: From the a Metric” drop-down, choose PD_whole_tree and from the a category” choose ID”. You “Select ‘Select “Sample will now see Faith’s Phylogenetic Diversity rarefication curves for all three sample sites. Which sample has the highest species richness? Do you believe we have sufficiently sampled this location in order to see all of its microbial diversity? Justify your answer. Change the metric to Species”. Does this metric support your conclusions in question 6? Explain. “Observed
Downloading Files Using Cyberduck Download the Centralia_Case_Study folder with all of your data to your Desktop instance using Cyberduck. Start Cyberduck. It is in your applications folder. Cyberduck allows you to transfer files between your computer and the Amazon EC2 instance you are running. Click on “Open Connection” in the upper left of the window, and choose SFTP from the top drop-down menu. Type the IP address for your EC2 instance (It is on the blackboard) into the Server window in Cyberduck. Type ubuntu (exactly as written!) as your username. You do not need a password. Click on ‘Use Public Key Authentication’ at the bottom of the Cyberduck window and then migrate to and choose your key pair (it should be on your desktop as QIIME-1.pem). Your Cyberduck window should now look something like the figure on the left. If it does, click on “Connect”. Then click on ‘allow’. A new window will open up in Cyberduck when it has connected to the server. To copy all of your Centralia files to your desktop, simply drag and drop your Centralia_Case_Study folder into the desktop of your computer. Say yes to replace the current folder. Copying these files may take a while, so go take a break if it does. Find your Centralia_Case_Study folder on your desktop and open it, and then open the rarification_plots folder. Double click on rarefication_plots.html to open it. You should see a browser window that looks like this: From the “Select a Metric” drop-down, choose PD_whole_tree and from the ‘Select a category” choose “Sample ID”. You will now see Faith’s Phylogenetic Diversity rarefication curves for all three sample sites. Which sample has the highest species richness? Do you believe we have sufficiently sampled this location in order to see all of its microbial diversity? Justify your answer. Change the metric to “Observed Species”. Does this metric support your conclusions in question 6? Explain.
centralia%20metagenomics%20case%20study%20part%203.docx