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

Im having HG 19 Sample ID, in this format

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

Want to know how to annotate this..

genome ngs chromosome chromosomal position
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updated by Jean-Karim Heriche Jean-Karim Heriche • written by bharathramh • bharathramh

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

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written by bharathramh • bharathramh

1 answer

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)

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written by Jean-Karim Heriche Jean-Karim Heriche

  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

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written by bharathramh • bharathramh

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.

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written by Jean-Karim Heriche Jean-Karim Heriche

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