Body: <p>I want to analyse the single-cell ATAC-seq data from 10X downloaded from GSE158398. The files attached to this dataset are <code>matrix.mtx.gz</code>, <code>fragments.tsv.gz</code>, and <code>barcodes.tsv.gz</code> files, in addition to a <code>peaks.bed.gz</code> file.</p>
  <p>How do I load this into R and make a Seurat object? Normally there is a matrix, barcodes and features files as output from scATAC-seq 10X data, so how do I handle only having a fragments file instead?</p>
  <p>Thank you very much for your help with this!</p>
  <p>Edit:</p>
  <p>This is the code I would normally run to load the ATAC counts (matrix), barcodes and features and make the Seurat object. However, with this dataset, I do not have the features.tsv file, but a fragments.tsv file instead and so I am unsure how to change my code to accommodate this change in input data.</p>
  <pre class="lang-r prettyprint-override"><code>ATAC_dir &lt;- &quot;~/GSE169246_PDL1/ATAC/&quot;
  
  barcode_path_ATAC &lt;- paste0(ATAC_dir, &quot;barcodes.tsv.gz&quot;)
  features_path_ATAC &lt;- paste0(ATAC_dir, &quot;features.tsv.gz&quot;)
  matrix_path_ATAC &lt;- paste0(ATAC_dir, &quot;matrix.mtx.gz&quot;)
  
  barcode_names_ATAC &lt;- read.delim(barcode_path_ATAC, 
                              header = FALSE, 
                              stringsAsFactors = FALSE)$V1
  
  feature_names_ATAC &lt;- read.delim(features_path_ATAC, 
                                   header = FALSE, 
                                   stringsAsFactors = FALSE)$V1
  
  mat_ATAC &lt;- readMM(file = matrix_path_ATAC)
  
  colnames(mat_ATAC) &lt;- barcode_names_ATAC
  rownames(mat_ATAC) &lt;- feature_names_ATAC
  
  
  chrom_assay &lt;- CreateChromatinAssay(
    counts = mat_ATAC,
    sep = c(&quot;:&quot;, &quot;-&quot;),
    genome = 'hg38',
    fragments = &quot;peaks.bed.gz&quot;,
    min.cells = 10,
    min.features = 200
  )
  
  seurat_ATAC &lt;- CreateSeuratObject(
    counts = chrom_assay,
    assay = &quot;peaks&quot;
  )
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-06-22T14:32:34.783Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-06-22T14:43:22.650Z
Comments.Text: Welcome to the site Ebla. Could you kindly describe the code you have written so far to load the data?
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-06-23T07:17:04.943Z
Comments.Text: Thank you, I have edited my original post now. I hope it is more clear now, please let me know if I can make it clearer
Comments.UserDisplayName: Embla
Tags: <seurat><single-cell><10x-genomics><atac-seq>
Title: Loading scATAC-seq data containing matrix.mtx, fragments.tsv and barcodes.tsv files from GEO into R?
ThreadText: # Loading scATAC-seq data containing matrix.mtx, fragments.tsv and barcodes.tsv files from GEO into R?
  
  (Asked by: username_0 on 2023-06-22)
  
  I want to analyse the single-cell ATAC-seq data from 10X downloaded from GSE158398. The files attached to this dataset are `matrix.mtx.gz`, `fragments.tsv.gz`, and `barcodes.tsv.gz` files, in addition to a `peaks.bed.gz` file.
  
  How do I load this into R and make a Seurat object? Normally there is a matrix, barcodes and features files as output from scATAC-seq 10X data, so how do I handle only having a fragments file instead?
  
  Thank you very much for your help with this!
  
  Edit:
  
  This is the code I would normally run to load the ATAC counts (matrix), barcodes and features and make the Seurat object. However, with this dataset, I do not have the features.tsv file, but a fragments.tsv file instead and so I am unsure how to change my code to accommodate this change in input data.
  
  ```r
  ATAC_dir <- "~/GSE169246_PDL1/ATAC/"
  
  barcode_path_ATAC <- paste0(ATAC_dir, "barcodes.tsv.gz")
  features_path_ATAC <- paste0(ATAC_dir, "features.tsv.gz")
  matrix_path_ATAC <- paste0(ATAC_dir, "matrix.mtx.gz")
  
  barcode_names_ATAC <- read.delim(barcode_path_ATAC, 
                              header = FALSE, 
                              stringsAsFactors = FALSE)$V1
  
  feature_names_ATAC <- read.delim(features_path_ATAC, 
                                   header = FALSE, 
                                   stringsAsFactors = FALSE)$V1
  
  mat_ATAC <- readMM(file = matrix_path_ATAC)
  
  colnames(mat_ATAC) <- barcode_names_ATAC
  rownames(mat_ATAC) <- feature_names_ATAC
  
  chrom_assay <- CreateChromatinAssay(
    counts = mat_ATAC,
    sep = c(":", "-"),
    genome = 'hg38',
    fragments = "peaks.bed.gz",
    min.cells = 10,
    min.features = 200
  )
  
  seurat_ATAC <- CreateSeuratObject(
    counts = chrom_assay,
    assay = "peaks"
  )
  
  ```
  
  **Tags:** seurat, single-cell, 10x-genomics, atac-seq
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_2**: Welcome to the site Ebla. Could you kindly describe the code you have written so far to load the data?  
  > **username_0**: Thank you, I have edited my original post now. I hope it is more clear now, please let me know if I can make it clearer  
  
  ---
  
  ## 0 answers
  
  