Metadata and sample identity¶

Metadata provides stable sample identity independently of FASTQ suffixes and drives grouping, color categories, and differential designs.

The first column must be named filename and map to input filenames after normalization. Additional columns describe biological and technical structure.

filename    genotype    stim    donor   replicate
NT_C_D1_A_S50_L003  NT  C   D1  A
NT_L_D1_A_S58_L003  NT  L   D1  A
KD24_C_D1_A_S54_L003    KD24    C   D1  A
KD24_L_D1_A_S62_L003    KD24    L   D1  A

Selectors accept comma-separated column names or one-based indices:

omnomnomics rna \
  -i EXPERIMENT \
  -g GRCh38 \
  -m metadata.tsv \
  --sample-name genotype,stim,donor,replicate \
  --sample-type genotype,stim \
  --sample-color genotype

• sample_id must uniquely identify each biological sample.
• sample_type defines analysis and track-hub groups.
• sample_color defines palette categories for non-stranded tracks.

Technical lanes are processed independently and merged at BAM level. Do not remove lane identity from filename; use sample_id derivation to identify the biological sample to which lanes belong.

For stranded RNA hubs, plus tracks are red and minus tracks are blue regardless of sample_color.