trace_to_matrix

Reliability status: stable

Output Files

For each trace file analyzed, the script generates:

  1. [tracefile]_Matrix_PWDscMatrix.npy: NUMPY single-cell pairwise-distance matrix.

  2. [tracefile]_Matrix_uniqueBarcodes.ecsv: Unique barcode list in ECSV format.

  3. [tracefile]_Matrix_Nmatrix.npy: NUMPY matrix containing the number of times each barcode pair is detected.

  4. [tracefile]_Matrix_Nmatrix.png: Plot of the N-matrix.

  1. [tracefile]_Matrix_HiMmatrix.png: Hi-M contact matrix calculated using a fixed threshold (default: 0.25 microns).

  1. [tracefile]_Matrix_PWDmatrixKDE.png: PWD KDE matrix plot.

  1. [tracefile]_Matrix_PWDmatrixMedian.png: PWD median matrix plot.

  1. [tracefile]_Matrix_PWDhistograms.png: Optional figure with distance distributions for each barcode pair. This file is written only when --plot_histograms is provided.

Examples

trace_to_matrix --help

Notes

  • See the command-line reference above for the complete option list.