Custom - Filter Significantly Expressed TranscriptsΒΆ

Select transcripts with significant change in expression according to user specified filters.

Location

  • Filepath: <SnakeLines_dir>/rules/paired_end/classification/differential_analysis/filter_significant/custom.snake
  • Rule name: custom__filter_significantly_expressed_transcripts

Input(s):

  • table: TSV table with statistical evaluation of change in expression
  • design: TSV table describing separation of samples into groups for differential expression

Output(s):

  • table: TSV table with transcripts with significant change in expression

Param(s):

  • max_fdr: Maximal value of fold discovery change for transcript to be reported
  • min_fold_change: Minimal value of fold change for transcript to be reported
  • reproducible_expression: At least one read must be mapped to transcript in all samples from over-expressed group to be reported