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README.md

@@ -19,7 +19,14 @@ under `analysis/`.
 
 ```text
 region_beds/
-  conservation_crossed/    regions crossed with conservation category
+  source/                  INPUT to the P4 enrichment analysis -- the four genomic
+                           regions, merged and cleaned:
+                           promoters_2kb.clean.merged.bed   (28,251 intervals)
+                           enhancers_dels.clean.merged.bed  (1,464,531)
+                           exon.clean.merged.bed            (402,955)
+                           intron.clean.merged.bed          (150,128)
+  conservation_crossed/    OUTPUT of that analysis, provided for checking: the four
+                           regions crossed with conservation category
                            {promoter,enhancer,exon,intron}_{conserved,neutral,accelerated}.bed
                            conservation_{conserved,neutral,accelerated}.bed
   simple/                  the same four regions without the conservation split
@@ -30,9 +37,11 @@ motifs/motifs.txt          JASPAR 2024 vertebrate motifs, thresholded to consens
                            sequences (PWM positions at 0.5, wildcards trimmed, <= 12 bp)
 ```
 
-`region_beds/conservation_crossed/` backs the P4 enrichment analysis (Figure 3);
-`ccre_classes/` backs the Multi-SCREEN task construction; `motifs/` backs the P1 motif
-preservation analysis (Figure 2A).
+`region_beds/source/` is what `analysis/enrichment/enrichment_heatmap.py` reads; it
+generates the conservation split and the crossed BEDs itself, so
+`region_beds/conservation_crossed/` is included only so results can be compared without
+re-running. `ccre_classes/` backs the Multi-SCREEN task construction; `motifs/` backs the
+P1 motif preservation analysis (Figure 2A).
 
 ## Not included — fetch these yourself