Search
Question: ENSEMBL database for annotatr
0
gravatar for xie186
9 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

ADD COMMENTlink modified 9 months ago by rcavalca130 • written 9 months ago by xie1860
0
gravatar for rcavalca
9 months ago by
rcavalca130
United States
rcavalca130 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

ADD COMMENTlink written 9 months ago by rcavalca130
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 342 users visited in the last hour