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

@@ -34,13 +34,21 @@ Now start up R, and we'll install the new packages:
     > install.packages("devtools")
     > library("devtools")
     > devtools::install_github("benjjneb/dada2", ref="v1.14")
+    # this step will take a while
     > install.packages("dada2",
                  repos = NULL,
                  type = "source",
-                 dependencies = c("Depends", "Suggests","Imports"))
+                 dependencies = c("Depends", "Suggests", "Imports"))
 
 ### 1.2 Processing our data with DADA2
 First let's go back to our data directory
 
-    > setwd("/bioinf/home/your_username/day_1/16S_amplicon/demultiplexed")
+    > setwd("/bioinf/home/your_username/day_1/16S_amplicons/demultiplexed")
+
+Then start dada2:
+
+    > library(dada2)
+
+The first parts of the process are now just preparing the files and file names.
+