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Rule sdgeAR_featurefilter:

Purpose

The sdgeAR_featurefilter filters the spatial digital gene expression (SGE) matrix by gene types, gene names, or the number of UMIs per gene.

Input Files

  • A Tab-delimited Feature File Required the feature file from Rule sdgeAR_reformat.

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) A Tab-delimited Clean Feature File

Description: A clean feature file (*.feature.clean.tsv.gz) that counts UMIs for features after gene-filtering.

File Naming Convention: 

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<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
ENSMUSG00000051285  Pcmtd1         1396  321   284  21     2
ENSMUSG00000057363  Uxs1           144   147   143  2      0
ENSMUSG00000097648  9330185C12Rik  1     55    1    8      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

No action is required.

Parameters

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downstream:               
 gene_filter:                                 
   keep_gene_type: "protein_coding|lncRNA"    
   rm_gene_regex: "^Gm\\d+|^mt-|^MT-"         
   min_ct_per_feature: 50

  • 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.

  • The min_ct_per_feature Parameter Defines the minimal UMI count for genes. Genes of which number of UMI is smaller than this cutoff will be removed.

Info

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

Dependencies

Given sdgeAR_featurefilter requires input from Rule sdgeAR_reformat, Rule sdgeAR_featurefilter can only execute after sdgeAR_reformat 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 c03_sdgeAR_featurefilter.smk.