Output Structure¶

After successful execution, your results/ directory will contain, for each sample:

results/
├── sample1.matched       # intermediate match output (removed by default)
├── sample1.annotated     # final annotated results
├── sample2.matched
└── sample2.annotated

---

File Type	Description
.matched	Intermediate tab-delimited file of read→reference matches. Marked temp in the Snakefile and deleted unless --notemp is used.
.annotated	Final annotated file per sample, with gene, TSS, CpG, and repeat annotations. Includes gene ID, feature type, TSS distance, CpG count, and repeat overlaps.