|
|
@@ -34,7 +34,7 @@ Note that this strategy is currently only available for `hg19`, `hg38`, `mm9` an
|
|
|
-Although CALDER was mainly tested on human and mouse dataset, it can be applied on dataset from other genomes. One additional information is required in such case: a `feature_track` that is presumably positively correlated with compartment score (or higher values in A than in B compartment). This information will be used for determining which branch of the hierachcal tree to be assigned as `A` compartment. Some suggested tracks are gene density, H3K27ac, H3K4me1, H3K4me2, H3K4me3, H3K36me3 (or negative transform of H3K9me3) signals. Note that this information will not alter the hierarchical compartment/TAD structure, and does not need to be coming from the same study as long as it comes from the same genome.
|
|
|
+Although CALDER was mainly tested on human and mouse dataset, it can be applied on dataset from other genomes. One additional information is required in such case: a `feature_track` that is presumably positively correlated with compartment score (thus higher values in A than in B compartment). This information will be used for determining which branch of the hierachcal tree to be assigned as `A` compartment. Some suggested tracks are gene density, H3K27ac, H3K4me1, H3K4me2, H3K4me3, H3K36me3 (or negative transform of H3K9me3) signals. Note that this information will not alter the hierarchical compartment/TAD structure, and does not need to be coming from the same study as long as it comes from the same genome.
|
Yuanlong LIU