Track hubs¶

Step 8 creates per-sample BigWigs and step 9 groups them into UCSC track hubs. Use metadata-driven sample_type to determine the hub grouping.

For samples such as NT_C_D1_A, NT_L_D1_A, KD24_C_D1_A, and KD24_L_D1_A, grouping by genotype,stim creates four hubs: NT_C, NT_L, KD24_C, and KD24_L.

omnomnomics rna \
  -i EXPERIMENT \
  -g GRCh38 \
  -j 8-9 \
  -m metadata.tsv \
  --sample-name genotype,stim,donor,replicate \
  --sample-type genotype,stim

RNA BigWigs are stranded. Plus-strand tracks use 255,0,0 and minus-strand tracks use 0,0,255; palette selection does not override these strand colors.

For ATAC and ChIP, --sample-color categories are mapped through the selected color table. Use the helper commands to create or inspect palettes:

omnomnomics create-track-color-table --help
omnomnomics display-track-color-table --help

The packaged palette directory is read-only. Supply a writable custom palette directory with -P when creating tables.