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

@@ -115,6 +115,7 @@ Like I said at the beginning, installation of DADA2 wasn't easy, and so in this
       seqtab <- data.frame(seqtab)
       colnames(seqtab) <- paste(taxtable[, 1], taxtable[, 2], taxtable[, 3], taxtable[, 4], 
       taxtable[, 5], taxtable[, 6], as.character(1:length(taxtable[, 1])), sep="-")
+      seqtab[, grep("Chloroplast|Mitochondria", colnames(seqtab), invert=TRUE)]
       seqtab <- seqtab/rowSums(seqtab)
       seqtab <- seqtab[, sapply(seqtab, function(x) max(x)) >= min_abund]
       seqtab$sample <- rownames(seqtab)