ScATAC-seq in the Cell Browser: Difference between revisions
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(First try at a cell browser atac page) |
(Removed older setting from item #2. (that line is no longer required).) |
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2. '''Add settings to cellbrowser.conf''' | 2. '''Add settings to cellbrowser.conf''' | ||
: After you've determined the GENCODE version add | : After you've determined the GENCODE version add this setting to the cellbrowser.conf: | ||
<pre> | <pre> | ||
atacSearch="mm10.gencode-M25" # Gencode version, use 'cbGenes fetch' to determine if your version is available | atacSearch="mm10.gencode-M25" # Gencode version, use 'cbGenes fetch' to determine if your version is available | ||
</pre> | </pre> | ||
Latest revision as of 14:09, 14 August 2025
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 this setting to the cellbrowser.conf:
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=matrixoption for cbBuild to rebuild the matrix and have cbBuild associate the peaks with gene symbols:
cbBuild -o alpha --redo=matrix
