A tool to convert genome coordinates and genome annotation files between assemblies.
Underneath, it uses the fantastic rtracklayer package from Bioconductor, and the chain files supplied by UCSC.
- it assumes a UCSC genome. Even if you install new chains based on Ensembl, there's hardcoded a
seqlevelsStyle(x) <- "UCSC"somewhere in the code. - poor handling of overlapping ranges. Formats like BigWig don't allow overlapping ranges. We're simply skipping them, which is really very poor handling. Be careful with that!