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Question: ENSEMBL database for annotatr
0
7 months ago by
xie1860
USA
xie1860 wrote:

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

modified 7 months ago by rcavalca120 • written 7 months ago by xie1860
0
7 months ago by
rcavalca120
United States
rcavalca120 wrote:

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