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

@@ -49,6 +49,14 @@ Then start dada2:
 
     > library(dada2)
 
-The first parts of the process are now just preparing the files and file names.
-
+The first parts of the process are now just preparing the files and file names. Look at the commands and the objects that are produced, and figure out what each one is doing.
+    
+    > path <- "."
+    > fnFs <- sort(list.files(path, pattern="R1.fastq.gz", full.names = TRUE))
+    > fnRs <- sort(list.files(path, pattern="R2.fastq.gz", full.names = TRUE))
+    > sample.names <- sapply(strsplit(basename(fnFs), ".R"), `[`, 1)
+    > filtFs <- file.path(path, "filtered", paste0(sample.names, "_F_filt.fastq.gz"))
+    > filtRs <- file.path(path, "filtered", paste0(sample.names, "_R_filt.fastq.gz"))
+    > names(filtFs) <- sample.names
+    > names(filtRs) <- sample.names