Practical-3-Processing-16S-rRNA-amplicon-data.md

@@ -24,7 +24,6 @@ Now, just to check which R we'll be using, run:
     $ which R
 
 You should see that the path is to the new R in your miniconda directory.
-
 Now it's time to download DADA2. This we'll do by downloading it from github:
 
     $ git clone https://github.com/benjjneb/dada2.git
@@ -32,9 +31,16 @@ Now it's time to download DADA2. This we'll do by downloading it from github:
 Now start up R, and we'll install the new packages:
 
     $ R
+    > install.packages("devtools")
+    > library("devtools")
+    > devtools::install_github("benjjneb/dada2", ref="v1.14")
     > install.packages("dada2",
                  repos = NULL,
                  type = "source",
                  dependencies = c("Depends", "Suggests","Imports"))
 
-### 1.2 
+### 1.2 Processing our data with DADA2
\ No newline at end of file
+First let's go back to our data directory
+
+    > setwd("/bioinf/home/your_username/day_1/16S_amplicon/demultiplexed")
+