Reports and Outputs

HOMERun keeps analysis categories directly under each species directory. Sample identity remains in filenames and TagDir names so multiple samples can share the same category directories safely.

project/
├── config.txt
├── logs/
├── logs_slurm/
└── homo_sapiens/
    ├── RawData/
    ├── Trimmed/
    ├── Aligned/
    ├── TagDirs/
    ├── bedGraphs/
    ├── TSS/
    ├── RITRIE/
    └── QC/
        └── K562/

Naming

Individual TagDirs and bedGraph directories use <sample>_<condition>_<assay>_<replicate>. Replicates that differ only by the final rN marker are also merged into a condition-preserving <sample>_<condition>_<assay>-combo directory.

For example, K562_D2_Post_csRNA_r1 and K562_D2_Post_csRNA_r2 produce K562_D2_Post_csRNA-combo; they are not merged with a D2_Pre condition.

TSS calls are written for matched individual replicates and their matched condition combos. csRNA is paired with the corresponding sRNA control and, when available, the corresponding total-RNA reference.

What to keep

Keep config.txt, TagDirs, bedGraphs, TSS results, and QC output with an archived analysis. If --cleanup-intermediates is enabled, Trimmed/ and Aligned/ data may be removed after QC has extracted its tables.