text: user6827: 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
  library(dplyr)
  library(Seurat) 
  library(ggplot2)
  
  -----------------------------------------------
  
  # 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
  
  #metadata
  #mf = metadata
  
  mf = metadata %>% filter(Type %in% c("PDAC", "NORMAL"))
  mf = mf %>% filter(!(ID %in% c("PDAC-HTB2854")))`
  
  
  user35: Seurat has a vignette specifically for combining multiple 10x libraries.
  
original_text: 6827: <p>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. </p>
  
  <p>For the <code>Read10x</code> command, is there a way to read multiple files at once, such as merging all the filter_featire_bc_matrix files?</p>
  
  <p>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?</p>
  
  <p>This is what I have thus far:</p>
  
  <pre><code># load the required libraries
  library(dplyr)
  library(Seurat) 
  library(ggplot2)
  
  -----------------------------------------------
  
  # 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
  
  #metadata
  #mf = metadata
  
  mf = metadata %&gt;% filter(Type %in% c("PDAC", "NORMAL"))
  mf = mf %&gt;% filter(!(ID %in% c("PDAC-HTB2854")))`
  </code></pre>
   35: <p>Seurat has <a href="https://satijalab.org/seurat/v3.1/merge_vignette.html" rel="nofollow noreferrer">a vignette specifically for combining multiple 10x libraries</a>.</p>
  