Open
Description
Examples:
- Names of files
- Number of files
- Number of raw reads input to workflow
- Number of reads after trimming and filtering
- Sequence table of read lengths and quantity of each
- Number of chimeras and percent of reads left
First take: http://benjjneb.github.io/dada2/tutorial.html#track-reads-through-the-pipeline
getN <- function(x) sum(getUniques(x))
track <- cbind(out, sapply(dadaFs, getN), sapply(mergers, getN), rowSums(seqtab), rowSums(seqtab.nochim))
colnames(track) <- c("input", "filtered", "denoised", "merged", "tabled", "nonchim")
rownames(track) <- sample.names
head(track)
## input filtered denoised merged tabled nonchim
## F3D0 7793 7113 7113 6600 6600 6588
## F3D1 5869 5299 5299 5078 5078 5067
## F3D141 5958 5463 5463 5047 5047 4928
## F3D142 3183 2914 2914 2663 2663 2600
## F3D143 3178 2941 2941 2575 2575 2550
## F3D144 4827 4312 4312 3668 3668 3527