Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-02-23T15:27:39.807Z
Answers.Text: 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.
Answers.UserDisplayName: mmpp
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Answers.CreationDate: 2020-02-24T02:05:58.620Z
Answers.Text: You don't have to keep the intermediate Seurat objects.
Answers.UserDisplayName: burger
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Answers.CreationDate: 2020-02-24T10:24:54.580Z
Answers.Text: 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.
Answers.UserDisplayName: haci
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Answers.CreationDate: 2020-02-24T17:54:07.633Z
Answers.Text: @haci How do I give a prefix or suffix?
Answers.UserDisplayName: mmpp
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Answers.CreationDate: 2020-02-28T22:37:15.873Z
Answers.Text: Note that a month later, they put out a new vignette about merging data sets which is more complex:  https://satijalab.org/seurat/pancreas_integration_label_transfer.html
Answers.UserDisplayName: swbarnes2
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Answers.CreationDate: 2020-02-29T23:10:01.620Z
Answers.Text: That vignette is over a year old. Also, it is for integration (batch correction), not simple merging of data sets.
Answers.UserDisplayName: burger
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Answers.CreationDate: 2020-03-01T15:16:23.567Z
Answers.Text: That's not what I'm looking for. Is there not a way to merge the counts from a directory and then create just one Seurat object?
Answers.UserDisplayName: mmpp
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-03-01T21:23:50.470Z
Answers.Text: See previous comment by @haci. However, there are many benefits of creating separate Seurat objects for each library, such as performing per-library QC.
Answers.UserDisplayName: burger
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Answers.UserDisplayName: burger
Body: <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>
  
Tags: <r><scrnaseq><seurat><10x-genomics>
Title: Reading multiple raw files in Seurat
ThreadText: # Reading multiple raw files in Seurat
  
  (Asked by: username_0 on 2020-02-23)
  
  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")))`
  
  ```
  
  **Tags:** r, scrnaseq, seurat, 10x-genomics
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-02-23. Score: 2
  
  Seurat has [a vignette specifically for combining multiple 10x libraries](https://satijalab.org/seurat/v3.1/merge_vignette.html).
  
  > **Comments:**
  > **username_0**: 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.  
  > **username_1**: You don't have to keep the intermediate Seurat objects.  
  > **username_2**: 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.  
  > **username_0**: @username_2 How do I give a prefix or suffix?  
  > **username_3**: Note that a month later, they put out a new vignette about merging data sets which is more complex:  https://satijalab.org/seurat/pancreas_integration_label_transfer.html  
  > **username_1**: That vignette is over a year old. Also, it is for integration (batch correction), not simple merging of data sets.  
  > **username_0**: That's not what I'm looking for. Is there not a way to merge the counts from a directory and then create just one Seurat object?  
  > **username_1**: See previous comment by @username_2. However, there are many benefits of creating separate Seurat objects for each library, such as performing per-library QC.  
  
  ---
  
  