Transcription Factor Motif Analysis

In this analysis, peaks are matched to a set of known transcription factor (TF) binding sites and for each cell barcode the fragment counts are grouped based on transcription factors their peaks are assigned to. This results in a more compact representation of chromatin accessibility patterns. To enable TF motif analysis, specify a database of position-weight matrices (PWM) corresponding to transcription factor motifs in JASPAR format:

DRAGEN will produce two files <prefix>.scATAC.motifs.matrix.mtx and <prefix>.scATAC.tf.motifs.tsv which combined with file <prefix>.scATAC.barcodes.tsv (also used in the cell-by-peak count matrix) represent the cell-by-TF count matrix in matrix market format.