Edger - Identify Transcripts With Changed ExpressionΒΆ

Compare counts of selected groups of samples and find features with significant change across the groups

Location

  • Filepath: <SnakeLines_dir>/rules/classification/differential_analysis/edger.snake
  • Rule name: edger__identify_transcripts_with_changed_expression

Input(s):

  • counts: Aggregated counts for each transcript and sample in tabular format
  • metadata: File with samples attributes - use for separating samples into compared groups

Output(s):

  • norm_counts: TSV table with normalised number of reads (by sample read depth)
  • table: TSV table with statistical evaluation of change of expression
  • design: TSV table describing separation of samples into groups for differential expression

Param(s):

  • group_by: attribute (in the metadata file header) that would split samples into two categories
  • batch: attribute (in the metadata file header) that would split samples categories with similar batch bias effect (e.g. samples from same sequencing run)