Interpreting the output of Single Cell ATAC-Seq Analysis
The main output of Single Cell ATAC-Seq Analysis is a Peak Count Matrix (
). This can be used directly in Cluster Single Cell Data, tSNE for Single Cell, and UMAP for Single Cell.
The Read Mapping (
) that was used for calling peaks is also produced. We recommend using this rather than the original read mapping in later analyses, because it is smaller and the shape of peaks can be seen more clearly.
The Motif Track (
) output shows the location of all transcription factor motifs found within peaks. Each row in the table view (
) contains the following information:
- Chromosome. The chromosome on which the motif was found.
- Region. The region matching the motif.
- Name. The name of the transcription factor.
- Score. The score for matching the region against the motif.
- Score threshold. The score threshold that must be reached for the match to be significant at p-value 0.0001. This is specific to each motif - for example, longer motifs will typically require a higher score to be as significant as shorter ones. All reported motifs have a score higher than the score threshold. The difference between the score and score threshold for several overlapping motifs may give an indication of which motif is the 'best fit' for a region.
- Footprint score. The footprint score at the middle of the motif. Higher scores show more evidence of transcription factor binding.
- Bound. "Yes" if the footprint score is higher than a threshold determined from the data, and otherwise "No". Only transcription factors for each peak that are bound are reported in the Peak Count Matrix.
The Footprint Graph Track (
) output shows the footprint score at all positions on the genome. This is mainly provided for visualization.
The Report (
) is useful for quality control, and is described separately in The report output from Single Cell ATAC-Seq Analysis.