Skip to content

Rule sdgeAR_reformat:

Purpose

Reformat the spatial digital gene expression (SGE) matrix from the 10x Genomics format to a FICTURE-compatible TSV format.

Input Files

  • Spatial Digital Gene Expression (SGE) Matrix and its Metadata File for Coordinates Required input files include a SGE matrix and its meta file for X Y coordinates. Those files are required to be stored in the sgeAR subfolder in the analysis directory. This could be generated by Rule sdge2sdgeAR or manually prepared by the users.

Output Files

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

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

(1) An SGE in a FICTURE-compatible Format

Description: A transcript-indexed SGE in the FICTURE format is generated, which contains all information including the barcode information, features information, and count for each genomic feature.

File Naming Convention: 

1
<unit_id>.transcripts.tsv.gz

File Format: 

1
2
3
4
#lane  tile  X     Y        gene_id             gene   gn  gt  spl  unspl  ambig
1      1     5982  1441004  ENSMUSG00000029368  Alb    1   1   1    0      0
1      1     8173  6873084  ENSMUSG00000053907  Mat2a  1   1   0    0      0
1      1     8729  6840669  ENSMUSG00000037071  Scd1   1   1   1    0      0

  • #lane: lane ID
  • tile: tile ID
  • X: X-coordinate
  • Y: Y-coordinate
  • gene_id: Gene Ensemble ID
  • gene: Gene symbol
  • gn: the count per gene per barcode for Gene
  • gt: the count per gene per barcode for GeneFull
  • spl: the count per gene per barcode for Spliced
  • unspl: the count per gene per barcode for Unspliced
  • ambig: the count per gene per barcode for Ambiguous

(2) A Tab-delimited Feature File

Description: This include a feature file (*.feature.tsv.gz) that counts UMIs for each gene.

File Naming Convention: 

1
<unit_id>.feature.tsv.gz

File Format:

1
2
3
4
gene_id             gene     gn    gt   spl  unspl  ambig
ENSMUSG00000100764  Gm29155  3     3    1    0      2
ENSMUSG00000100635  Gm29157  0     0    0    0      0
ENSMUSG00000100480  Gm29156  0     0    0    0      0
  • gene_id: Gene Ensemble ID
  • gene: Gene symbol
  • gn: the count per gene per barcode for Gene
  • gt: the count per gene per barcode for GeneFull
  • spl: the count per gene per barcode for Spliced
  • unspl: the count per gene per barcode for Unspliced
  • ambig: the count per gene per barcode for Ambiguous

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_reformat 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 c02_sdgeAR_reformat.smk.