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16S_2023.ipynb

@@ -205,7 +205,7 @@
         "```\n",
         "qiime plugin action --i-argument1 ... --o-argument2 ...\n",
         "```\n",
-        "In the previous command, we are calling the ```tools``` plugin within QIIME2 to ipmport our data. The following arguments designate where the manifest is, as well as where the output should be saved. We also tell QIIME what sort of input to expect.\n",
+        "In the previous command, we are calling the ```tools``` plugin within QIIME2 to import our data. The following arguments designate where the manifest is, as well as where the output should be saved. We also tell QIIME what sort of input to expect.\n",
         "\n",
         "Argument types usually begin with a letter denoting their meaning:\n",
         "\n",
@@ -246,7 +246,7 @@
         "\n",
         "## Quality Filtering\n",
         "\n",
-        "Before we can use our sequencing data, we need to \"denoise\" it. To do this, we'll use a plug-in called DADA2. This involves three things.\n",
+        "Before we can use our sequencing data, we need to \"denoise\" it. To do this, we'll use a plugin called DADA2. This involves three things.\n",
         "\n",
         "1. filter and trim the reads\n",
         "2. find the most likely set of unique sequences in the sample (ASVs)\n",
@@ -412,7 +412,7 @@
       "source": [
         "\n",
         "## Calculating Diversity\n",
-        "Using the Diversity plugin, we can use our table and tree to calculate several diversity metrics. To account for variations in sampling depth, we'll provide QIIME with a cutoff at which rarefy all our samples. We'll also pass in our metadata file, so we can keep track how which samples come from each group."
+        "Using the Diversity plugin, we can use our table and tree to calculate several diversity metrics. To account for variations in sampling depth, we'll provide QIIME with a cutoff at which rarefy all our samples. Since this randomly selects sequences, your results might look a little different. We'll also pass in our metadata file, so we can keep track how which samples come from each group."
       ]
     },
     {
@@ -439,7 +439,7 @@
       "source": [
         "## Alpha Diversity\n",
         "\n",
-        "We get a bunch of outputs from the previous command - measures of both alpha and beta diversity. To start, let's use the Shannon vector in the output directory to create a visualization of alpha diversity across samples. enerally, healthy, long-living individuals have balanced diverse microbiomes. However, this isn't necessarily a direct indicator of health or disease. Let's see how it looks in our samples"
+        "We get a bunch of outputs from the previous command - measures of both alpha and beta diversity. To start, let's use the Shannon vector in the output directory to create a visualization of alpha diversity across samples. Generally, healthy, long-living individuals have balanced diverse microbiomes. However, this isn't necessarily a direct indicator of health or disease. Let's see how it looks in our samples"
       ]
     },
     {
@@ -476,7 +476,7 @@
         "\n",
         "<br>\n",
         "\n",
-        "We can check for 'signficant' separation between samples using PERMANOVA. We can do this with the diversity plug-in in QIIME2."
+        "We can check for 'significant' separation between samples using PERMANOVA. We can do this with the diversity plugin in QIIME2."
       ]
     },
     {
@@ -662,9 +662,7 @@
         "\n",
         "1) Are some of the branch lengths on the tree longer than you would expect? Do you notice anything interesting or suspicious about the taxonomic identities of these branches?\n",
         "\n",
-        "2) Can you find examples of phyla that are polyphyletic (i.e. where clusters of ASVs from the same phylum are found in different locations on the tree, showing different commmon ancestors)? What about polyphyletic taxa at lower taxonomic levels, like at the family or genus levels? Why do you think these patterns exist?\n",
-        "\n",
-        "3) Use the \"Shear Tree\" functionality to only visualize the phylogenetic tree of the genus *Prevotella*. What do you observe? Can you figure out which of the unique V4 sequences are found only in one population? What impact might this have on studies trying to link *Prevotella* to human health?"
+        "2) Can you find examples of phyla that are polyphyletic (i.e. where clusters of ASVs from the same phylum are found in different locations on the tree, showing different commmon ancestors)? What about polyphyletic taxa at lower taxonomic levels, like at the family or genus levels? Why do you think these patterns exist?"
       ],
       "metadata": {
         "id": "WPMlG8w9aCsW"