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Rule sdgeAR_reformat:

Purpose

The sdgeAR_reformat prepares the spatial digital gene expression matrix (SGE) in FICTURE-compatible format. This rule also offers gene-filtering function, when preparing the FICTURE-compatible SGE, depends on the user-defined parameters in the job configuration file.

Input Files

  • Spatial Digital Gene Expression Matrix (SGE) and its Metadata File for Coordinates Required input files include a SGE file 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: 

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

(1) FICTURE-compatible SGE

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

File Naming Convention: 

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<unit_id>.merged.matrix.tsv.gz

File Format: 

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#lane  tile  X      Y        gene_id             gene    gn  gt  spl  unspl  ambig
1      1     5982   1439022  ENSMUSG00000029368  Alb     1   1   1    0      0
1      1     8173   6863206  ENSMUSG00000053907  Mat2a   1   1   0    0      0
1      1     8729   6830792  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) Two Tab-delimited Feature Files

Description: This include a feature file (*.feature.tsv.gz) that contains information for all features and another feature file (*.feature.clean.tsv.gz) that contains information for features aftering the gene-filtering.

File Naming Convention: 

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<unit_id>.feature.tsv.gz 
<unit_id>.feature.clean.tsv.gz

File Format: Those two feature files share the same format:

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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

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downstream:               
  gene_filter:            
   keep_gene_type: "protein_coding,lncRNA"    # genes to keep
   rm_gene_regex: "^Gm\\d+|^mt-|^MT-"         # genes to remove

  • The keep_gene_type Parameter Specifies the types of genes to retain during gene filtering.

  • The rm_gene_regex Parameter Defines the types of genes to be excluded during gene filtering.

Info

It is important to note that both parameters utilizes regular expressions.

Dependencies

Given sdgeAR_reformat requires input from Rule sdge2sdgeAR, Rule sdgeAR_reformat can only execute after sdge2sdgeAR and its prerequisite rules have successfully completed their operations. See an overview of the rule dependencies in the Workflow Structure.

Code Snippet

The code for this rule is provided in a07_sdgeAR_reformat.smk.