1_demux.R

######################################
### demux2 for downstream analysis ###
######################################
library(Matrix)
library(tidyverse)
library(parallel)
library(data.table)



rm(list=ls())

outdir <- "./1_demux_output/"
if (!file.exists(outdir)) dir.create(outdir, showWarnings=F)

#################################
### 1. folders of counts data ###
#################################
basefolder <- "../counts_cellranger-2022-01-23/demuxlet/demuxlet/"
demuxfn <- list.files(basefolder,pattern="*.out.best")

expNames <- gsub(".out.best", "", demuxfn) 

############################
### 2, read demuxlet data ###
############################

# new column "NEW_BARCODE" was added to the data frame associated to each experiment (experiment name+barcode) "-1" was removed from end of barcode
demux <- mclapply(expNames,function(ii){
  cat("#Loading ", ii, "\n")
  fn <- paste0(basefolder, ii,".out.best")
  dd <- data.frame(fread(fn,header=T))
  dd <- dd%>%mutate(NEW_BARCODE=paste0(ii,"_", gsub("-1","",BARCODE)),EXP=ii)
},mc.cores=10)

# merging all the experiments 
demux <- do.call(rbind,demux)

### output
opfn <- paste0(outdir,"1_demux_New.ALL.rds");
write_rds(demux, opfn)

# DROPLET.TYPE: "SNG" "AMB"
opfn <- paste0(outdir,"1_demux_New.SNG.rds");
demux %>% filter(DROPLET.TYPE=="SNG") %>%
    write_rds(opfn)