Rule `sdgeAR_minmax`:¶

Purpose¶

Create a meta file containing the X and Y coordinates for a raw SGE matrix generated by Rule sdgeAR_reformat. For a filtered SGE matrix, this meta file will be produced by Rule sdgeAR_polygonfilter and is likely to be used in downstream analysis. Therefore, this rule ensures that a coordinate meta file is available for the raw SGE matrix.

Input Files¶

A SGE in FICTURE-compatible Format A transcript-indexed SGE in the FICTURE format, which is generated by Rule sdgeAR_reformat.

Output Files¶

The rule generates the following output in the specified directory path:

1	`<output_directory>/analysis/<run_id>/<unit_id>/preprocess`

(1) A Metadata File for X Y Coordinates¶

Description: This file contains the minimum and maximum X Y coordinates for the raw SGE matrix.

File Naming Convention:

1	`<unit_id>.<solo_feature>.raw.coordinate_minmax.tsv`

* <solo_feature>: Genomic feature.

File Format:

xmin    -27.973391144511698
xmax    8699.068916753664
ymin    -26.25
ymax    5144.932078838597

- xmin: The minimum x-coordinate in micrometers across all barcodes in the raw SGE matrix. - xmax: The maximum x-coordinate in micrometers across all barcodes in the raw SGE matrix. - ymin: The minimum y-coordinate in micrometers across all barcodes in the raw SGE matrix. - ymax: The maximum y-coordinate in micrometers across all barcodes in the raw SGE matrix.

Output Guidelines¶

The output file could be used as the input for FICTURE.

Parameters¶

No additional parameter is applied in this rule.

Dependencies¶

Rule sdgeAR_minmax executes only after sdge2sdgeAR and its prerequisites are completed. See the Workflow Structure for dependencies.

Code Snippet¶

The code for this rule is provided in c03_sdgeAR_minmax.smk.

Rule sdgeAR_minmax:¶