ScATAC-seq in the Cell Browser

Working with single-cell ATAC-seq data in the Cell Browser is straightforward.

1. Pick a GENCODE version

You should preferably pick the version of GENCODE used in the analysis. If that's not available (e.g. GENCODE v22), then picking the next closest (e.g. GENCODE v23) should be fine. In addition to the version, ensure you're looking at the right assembly (e.g. hg19 vs hg38).

2. Add settings to cellbrowser.conf

After you've determined the GENCODE version add these settings to the cellbrowser.conf:

geneLabel="Peak" # Changes label for 'Gene' tab to 'Peak'
atacSearch="mm10.gencode-M25" # Gencode version, use 'cbGenes fetch' to determine if your version is available

3. Build the dataset

Now you can build the dataset:

cbBuild -o alpha

If you've already build the dataset previously, then you'll need to use the --redo=matrix option for cbBuild to rebuild the matrix and have cbBuild associate the peaks with gene symbols:

cbBuild -o alpha --redo=matrix