Informative KMER-based workflow • Zorn

First set up your Zorn/Bascet workdirectory as before. If you wish to run these steps on a SLURM cluster, see separate vignette and adapt accordingly.

library(Zorn)
bascet_runner.default <- LocalRunner(direct = TRUE, show_script=TRUE)
bascetRoot <- "/home/yours/an_empty_workdirectory"

(SLURM-compatible step)

### Compute minhashes for each cell
BascetComputeMinhash(
  bascetRoot
)

### Gather minhashes into a single histogram
BascetMakeMinhashHistogram(
  bascetRoot
)

kmer_hist <- BascetReadMinhashHistogram(bascetRoot)

kmer_hist$rank <- 1:nrow(kmer_hist)
ggplot(kmer_hist[kmer_hist$cnt>2,], aes(rank, cnt)) +
  geom_point() +
  scale_x_log10() +
  scale_y_log10()

### Pick KMERs
useKMERs <- kmer_hist$kmer[kmer_hist$cnt>5]

### Build count table by looking up selected KMERs in per-cell KMER databases
BascetQueryFq(
  bascetRoot,
  useKMERs=useKMERs
)