I have multiple single cell samples to analyze and I'm following the instructions in Satija Lab's website. I want to merge all the count files from all the samples at once, and associate the metadata to each sample.

For the Read10x command, is there a way to read multiple files at once, such as merging all the filter_featire_bc_matrix files?

I have all the samples saved in a directory on my desktop, is it possible to call the directory within the script for it to read all the raw counts?

This is what I have thus far:

# load the required libraries


# set up the working directory

wd = ("~/Seurat") setwd(wd)

# read all metadata

metadata = read.table("metadata_Jan2020.csv", sep=';', header=T, stringsAsFactors=F)
rownames(metadata) = metadata$LibraryID

#mf = metadata

mf = metadata %>% filter(Type %in% c("PDAC", "NORMAL"))
mf = mf %>% filter(!(ID %in% c("PDAC-HTB2854")))`

1 Answer 1


Seurat has a vignette specifically for combining multiple 10x libraries.

  • $\begingroup$ Yes, I know. But I'm wondering if there is a way to merge all counts before creating a Seurat object. I'd like to just create one Seurat object with all the counts. $\endgroup$
    – mmpp
    Feb 23, 2020 at 15:27
  • $\begingroup$ You don't have to keep the intermediate Seurat objects. $\endgroup$
    – burger
    Feb 24, 2020 at 2:05
  • $\begingroup$ To merge all counts before creating individual Seurat objects, you will need to give a prefix or a suffix to cell names. I would however advise to create individual Seurat objects with apply() or mclapply() and then reduce() these with Seurat's merge(), this will give you a single Seurat object with all your samples. $\endgroup$
    – haci
    Feb 24, 2020 at 10:24
  • $\begingroup$ @haci How do I give a prefix or suffix? $\endgroup$
    – mmpp
    Feb 24, 2020 at 17:54
  • $\begingroup$ Note that a month later, they put out a new vignette about merging data sets which is more complex: satijalab.org/seurat/pancreas_integration_label_transfer.html $\endgroup$
    – swbarnes2
    Feb 28, 2020 at 22:37

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