Edger - Identify Transcripts With Changed Expression

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

Location

• Filepath: <SnakeLines_dir>/rules/paired_end/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)

Edger - Convert Summary Tsv Table To Xlsx

Convert summary.normed.tsv table to Excel format.

Location

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

Input(s):

• tsv_table: Table in tsv format

Output(s):

• xlsx_table: Table in Excel format