d352dbd221f92bc4008d1f7c91fbf5cc98f36908
max
  Thu Jul 31 07:21:29 2025 -0700
adding atac docs for marc

diff --git docs/howto.rst docs/howto.rst
index 2722103..27ee0dc 100644
--- docs/howto.rst
+++ docs/howto.rst
@@ -388,47 +388,52 @@
 
 How to visualize single-cell ATAC-seq data in the Cell Browser
 ^^^^
 
 The Cell Browser supports single-cell ATAC-seq data. It requires the same files that a standard dataset needs with the added requirement of knowing the gene models to enable searching for peaks around genes. Typically ATAC-seq data includes inferred gene signal analysis as well, so the gene models used for that should be the same used here.
 
 Step 1: Gather required files
 """"
 
 You will the following three files:
 
 * Expression matrix with cell names as columns and peak ranges as rows. 
 * Cell annotations/metadata
 * Layout coordinats (e.g. UMAP)
 
+The peaks must be encoded in the expression matrix in the format chr:start-end, e.g. "chr1:1000-2000".
+
 Step 2: Download the gene model files
 """"
 
 Pick a current gene model version, either by asking the authors or use current
 one. Use ``cbGenes fetch`` to list the gene model files we have prebuilt for you at UCSC, then
 use ``cbGenes fetch`` followed by the name of the file to download it. Also download the
 gene symbol <-> ID mapping to the user can search for both gene IDs and gene symbols.
 
 Examples:
 
 ::
 
  cbGenes fetch gencode-34        # geneId -> symbol mapping for human gencode relase 34
  cbGenes fetch hg38.gencode-34   # gene -> chrom mapping for human gencode relase 34
 
 Both files are required for this to work.
 
+We provide a few odd gene model files, e.g. C. elegans or brine shrimp, these are documented at 
+https://cells-test.gi.ucsc.edu/downloads/cellbrowserData/genes/README.txt
+
 Step 3: Set up your cellbrowser.conf
 """"
 
 You will need to add the following lines to your ``cellbrowser.conf``:
 
 ::
 
  atacSearch = "hg38.gencode-34" # Version downloaded in Step 3 combined with the UCSC assembly name
  geneLabel = "Peak" 
 
 You will still need to set the other `required settings <https://github.com/maximilianh/cellBrowser/blob/master/src/cbPyLib/cellbrowser/sampleConfig/cellbrowser.conf#L1>`_ in your cellbrowser.conf as well
 
 Step 5: Build your Cell Browser
 """"