Hi Raymond,

For Annotatr, it seems that it uses UCSC know genes as the database, right? Is there an easy way that I can use ENSEMBL database?

The function read_regions will add one base on the left side of the coordinates, right? If the coordinate is 1 100 200, it will be 1 101 200 after reading using read_regions.

Best, Shaojun

Hello,

Correct, annotatr uses the UCSC knownGenes database. If there was a TxDb package for hg19 that used ENSEMBL as its basis, it would be fairly easy to create the annotations, but I am not aware of such a TxDb package.

As to your question about read_regions(), my understanding is that 1 is added to the start coordinate by rtracklayer::import because BED is 0-based start and 1-based end, while GRanges are supposed to be 1-based start and end.

Raymond