How to get the annotations (Gene name,Gene Function-introns,exons,Transcript id..) from chromosomal position

Question

[bharathramh]

Im having HG 19 Sample ID, in this format

**chr19:56037269:56037284
chr19:57191411:57191434**

Want to know how to annotate this..

[BioinfGuru]

Consider ChIPpeakAnno

You may need to edit the format of the file

[bharathramh]

I have tried with that, But I donno how 2 do :/ Can You suggest me some other Tools?!

[BioinfGuru]

Can you give an idea of what the problem was?

ChIPpeakAnno quick start

Answer 1

[Jean-Karim Heriche]

If this corresponds to a species present in Ensembl, use the Ensembl API or Ensembl's BioMart to retrieve annotations for each region (maybe via the biomaRt bioconductor package)

[bharathramh]

1. Im not able to find the function of the specific region(say inton,exon,UTR) in Ensembl.

2. And Also Im not able to get it for each specific chromosomal ID, Like if chromosomal position which Im having are fall under 1 gene it showing 1 gene in result, (i have unn

[Jean-Karim Heriche]

A genomic region in Ensembl is called a slice so look at the Slice object in the API. The idea is that you extract a slice then look for features on it. Check this tutorial.