SampleData PairedEndSequencesWithQuality processing - Revision history

Bes: /* Command set 11 - visualizing the bacteria names */

2022-07-12T15:51:21Z

Command set 11 - visualizing the bacteria names

Bes: /* Visualizing the barplot */

2022-07-07T22:58:40Z

Visualizing the barplot

Bes: /* Command set 9 */

2022-07-07T22:58:23Z

Command set 9

Bes: /* Command set 11 - visualizing the bar plot */

2022-07-07T22:57:30Z

Command set 11 - visualizing the bar plot

Bes: /* Command set 8 */

2022-07-07T22:56:34Z

Command set 8

Bes: /* Command set 7 */

2022-07-07T22:52:48Z

Command set 7

Bes: /* Command set 7 - visualizing the sequence data (Optional) */

2022-07-07T22:35:25Z

Command set 7 - visualizing the sequence data (Optional)

Bes: /* Command set 6 - visualize the "FeatureTable" data (Optional) */

2022-07-07T22:35:10Z

Command set 6 - visualize the "FeatureTable" data (Optional)

Bes: /* Command set 6 - visualizing the sequence data (Optional) */

2022-07-07T22:34:26Z

Command set 6 - visualizing the sequence data (Optional)

Bes: /* Command set 6 */

2022-07-07T22:34:08Z

Command set 6

@@ Line 132: / Line 132: @@
     --o-classification taxonomy.qza <enter>
-====Command set 11 - visualizing the bacteria names====
+====Command set 11 - visualizing the bacteria names (Optional)====
     qiime metadata tabulate \
     --m-input-file taxonomy.qza \

← Older revision		Revision as of 22:58, 7 July 2022
Line 146:		Line 146:
	--o-visualization taxa-bar-plots.qzv <enter>		--o-visualization taxa-bar-plots.qzv <enter>

−	~~====Visualizing the barplot====~~
	Now drag and drop the taxa-bar-plots.qzv file into the view.qiime2.org/ window.		Now drag and drop the taxa-bar-plots.qzv file into the view.qiime2.org/ window.

@@ Line 137: / Line 137: @@
     --o-visualization taxonomy.qzv
-====Command set 9====
+====Command set 12 - visualizing the bar plot====
 Now we want to visualize this data using the barplot…using these commands:
-    qiime taxa barplot \
+    qiime taxa barplot \ <enter>
-    --i-table table-dada2.qza \
+    --i-table table-dada2.qza \ <enter>
-    --i-taxonomy taxonomy.qza \
+    --i-taxonomy taxonomy.qza \ <enter>
     --m-metadata-file sample-metadata.tsv \ <-- skip this line
-    --o-visualization taxa-bar-plots.qzv
+    --o-visualization taxa-bar-plots.qzv <enter>
 ====Visualizing the barplot====
 Now drag and drop the taxa-bar-plots.qzv file into the view.qiime2.org/ window.

@@ Line 132: / Line 132: @@
     --o-classification taxonomy.qza <enter>
-====Command set 11 - visualizing the bar plot====
+====Command set 11 - visualizing the bacteria names====
     qiime metadata tabulate \
     --m-input-file taxonomy.qza \

@@ Line 121: / Line 121: @@
 not totally sure what the above commands have done for us...
-====Command set 8====
+====Command set 10 - classifying the bacterial sequences====
-For the next command you will need to acquire a "classifier" file from [https://data.qiime2.org/2022.2/common/gg-13-8-99-515-806-nb-classifier.qza here_1] or [https://data.qiime2.org/2022.2/common/gg-13-8-99-nb-classifier.qza here_2] <-- this file needs to be saved/relocated into the main working folder.
+For the next command you will need to acquire a "classifier" file from [https://data.qiime2.org/2022.2/common/gg-13-8-99-515-806-nb-classifier.qza here_515-806] or [https://data.qiime2.org/2022.2/common/gg-13-8-99-nb-classifier.qza here_all 1500] <-- this file needs to be saved/relocated into the main working folder.
 On to taxonomy…to determine the taxonomic composition of the samples use the following commands:
-    qiime feature-classifier classify-sklearn \
+    qiime feature-classifier classify-sklearn \ <enter>
-    --i-classifier gg-13-8-99-515-806-nb-classifier.qza \ <-- us this line if using gg-13-8-99-515-806-nb-classifier.qza
+    --i-classifier gg-13-8-99-515-806-nb-classifier.qza \ <enter> '''OR'''
-    --i-classifier gg-13-8-99-nb-classifier.qza \ <-- us this line if using gg-13-8-99-nb-classifier.qza
+    --i-classifier gg-13-8-99-nb-classifier.qza \ <enter>
-    --i-reads rep-seqs-dada2.qza \
+    --i-reads rep-seqs-dada2.qza \ <enter>
-    --o-classification taxonomy.qza
+    --o-classification taxonomy.qza <enter>
     qiime metadata tabulate \
     --m-input-file taxonomy.qza \

@@ Line 109: / Line 109: @@
 Dragging and dropping this file into view.qiime2.org allows you to see the sequence for all the bacteria in your sample. There is no immediate need to view this data.
-====Command set 7====
+====Command set 9 - (SKIP/Optional)====
 Now we are ready to generate a tree for phylogenetic diversity using the following commands:
@@ Line 119: / Line 119: @@
     --o-rooted-tree rooted-tree.qza
-not totally sure what the above commands have done for us, but…
+not totally sure what the above commands have done for us...
 ====Command set 8====

@@ Line 100: / Line 100: @@
     --m-sample-metadata-file sample-metadata.tsv
-====Command set 7 - visualizing the sequence data (Optional)====
+====Command set 8 - visualizing the sequence data (Optional)====
 Next, we want to visualize the sequence data (rep-seqs-dada2.qza) by entering the following command:

@@ Line 96: / Line 96: @@
     --o-visualization table.qzv <enter>
+====Command set 7 - SKIP====
 The following command was listed in the tutorial, but was not used??? The .TSV file can be downloaded from the view.qiime2.org/table.qzv if we need it. Skip the following for now:
     --m-sample-metadata-file sample-metadata.tsv

@@ Line 100: / Line 100: @@
     --m-sample-metadata-file sample-metadata.tsv
-====Command set 6====
+====Command set 6 - visualizing the sequence data (Optional)====
-Next, we want to visualize the seq data (rep-seqs-dada2.qza) by entering the following command:
+Next, we want to visualize the sequence data (rep-seqs-dada2.qza) by entering the following command:
-    qiime feature-table tabulate-seqs \
+    qiime feature-table tabulate-seqs \ <enter>
-    --i-data rep-seqs-dada2.qza \
+    --i-data rep-seqs-dada2.qza \ <enter>
-    --o-visualization rep-seqs-dada2.qzv
+    --o-visualization rep-seqs-dada2.qzv <enter>
 ====Command set 7====