sc_editMatrix.py¶
Generate heatmaps to visualize error-corrected nucleotide changes in cell barcodes and UMIs. Shows the position (X-axis), type of edit (Y-axis, e.g., C→T), and frequency (color).
Usage¶
Options¶
| Option | Description | Default |
|---|---|---|
-i, --infile | Input BAM file | Required |
-o, --outfile | Prefix of output files | Required |
--limit | Number of alignments to process | All |
--cr-tag | BAM tag for raw cellular barcode | CR |
--cb-tag | BAM tag for corrected cellular barcode | CB |
--ur-tag | BAM tag for raw UMI | UR |
--ub-tag | BAM tag for corrected UMI | UB |
--cell-width | Cell width (points) in heatmap | 15 |
--cell-height | Cell height (points) in heatmap | 10 |
--font-size | Font size (points) | 8 |
--angle | Column label angle (0, 45, 90, 270, 315) | 45 |
--text-color | Color of cell numbers | black |
--file-type | Output format: pdf, png, tiff, bmp, jpeg | |
--verbose | Print detailed running information | Off |
--no-num | Omit numerical values from cells | Off |
Output¶
Heatmap files showing barcode and UMI error correction patterns.