In LarsenLab/immuntools: Larsen lab data analysis toolbox

library(DropletUtils)
library(Seurat)

# work on params to export variable from R to bash
Sys.setenv(fd_s3 = params$fd_s3) 
Sys.setenv(fd_sce = params$fd_sce)
Sys.setenv(fd_se = params$fd_se)

SCE

sync file from s3 to ec2

system("aws s3 sync $fd_s3 $fd_sce --region us-east-2")

unzip and rename files for SCE format

gunzip "${fd_sce}barcodes.tsv.gz"
gunzip "${fd_sce}matrix.mtx.gz"
gunzip "${fd_sce}features.tsv.gz"
mv "${fd_sce}features.tsv" "${fd_sce}genes.tsv"

create and save sce object

sce_obj <- read10xCounts(params$fd_sce)
save(sce_obj, file = params$obj_sce)
rm(sce_obj)

Seurat

sync file from s3 to ec2

system("aws s3 sync $fd_s3 $fd_se --region us-east-2")

create and save Seurat object

dat <- Read10X(data.dir = params$fd_se) 
rownames(x = dat[["Antibody Capture"]]) <- gsub(pattern = "_TotalSeqC", replacement = "", x = rownames(x = dat[["Antibody Capture"]]))

se_obj <- CreateSeuratObject(counts = dat[["Gene Expression"]])
se_obj[["ADT"]] <- CreateAssayObject(counts = dat[["Antibody Capture"]][, colnames(se_obj)])

save(se_obj, file = params$obj_se)
rm(dat, se_obj)

LarsenLab/immuntools documentation built on July 19, 2023, 9:43 a.m.