Qiime2 Instructions - Revision history

Bozz: /* Command set 1 */

2022-07-07T15:23:16Z

Command set 1

2022-07-06T19:28:33Z

Command set 8

2022-07-06T16:32:12Z

Command set 1

2022-07-05T21:47:22Z

Command set 3

2022-07-05T20:37:39Z

Command set 1

2022-06-22T20:50:20Z

Command set 9

2022-06-22T20:43:51Z

Command set 9

2022-06-22T20:43:17Z

Command set 8

2022-06-22T20:25:58Z

Command set 8

2022-06-22T20:24:12Z

Command set 8

← Older revision		Revision as of 15:23, 7 July 2022
Line 28:		Line 28:
	For VR laptops...		For VR laptops...

−	conda activate ~~/root/miniconda3/envs/~~qiime2-2022.2	+	conda activate qiime2-2022.2

@@ Line 116: / Line 116: @@
 ====Command set 8====
-For the next command you will need to acquire a "classifier" file from [https://data.qiime2.org/2018.2/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_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.
 On to taxonomy…to determine the taxonomic composition of the samples use the following commands:

@@ Line 25: / Line 25: @@
 ====Command set 1====
 The following commands must be executed using a terminal window/shell from the directory immediately above the ‘reads’ directory. The following assumes that Qiime2 has been installed on your computer. If you are just opening a terminal window, you must enter into the Qiime2 environment by typing:
   conda activate qiime2-202X.X <—where the X.X is your installed version; this is qiime2-2021.4 or qiime2-2022.2 (MAC), qiime2-2021.8  on the PC in CSB 360.

@@ Line 47: / Line 47: @@
    --o-visualization demux-paired-end_viz.qzv
-This output file, demux-paired-end_vis.qzv is then “dragged and dropped” into the https://view.qiime.org window and data will be displayed.
+This output file, demux-paired-end_vis.qzv is then “dragged and dropped” into the https://view.qiime2.org window and data will be displayed.
 Interpreting the .qzv data

@@ Line 26: / Line 26: @@
 The following commands must be executed using a terminal window/shell from the directory immediately above the ‘reads’ directory. The following assumes that Qiime2 has been installed on your computer. If you are just opening a terminal window, you must enter into the Qiime2 environment by typing:
-  conda activate qiime2-2021.4 <—where the .4 is the version; this is .8 on the PC in CSB 360.
+  conda activate qiime2-202X.X <—where the X.X is your installed version; this is qiime2-2021.4 or qiime2-2022.2 (MAC), qiime2-2021.8  on the PC in CSB 360.
   - the above commend will then result in the terminal window showing a (quine2-2021.4) line header.

@@ Line 126: / Line 126: @@
 ====Command set 9====
-Now we want to visulaize this data using the barplot…using these commands:
+Now we want to visualize this data using the barplot…using these commands:
     qiime taxa barplot \
@@ Line 133: / Line 133: @@
     --m-metadata-file sample-metadata.tsv \ <-- skip this line
     --o-visualization taxa-bar-plots.qzv

@@ Line 116: / Line 116: @@
     qiime feature-classifier classify-sklearn \
-    --i-classifier gg-13-8-99-515-806-nb-classifier.qza \
+    --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
-::::::OR
+    --i-classifier gg-13-8-99-nb-classifier.qza \ <-- us this line if using gg-13-8-99-nb-classifier.qza
     --i-reads rep-seqs-dada2.qza \
     --o-classification taxonomy.qza