Question: Intron cordinates requires for known exons
gravatar for HK
2.1 years ago by
HK40 wrote:

Hey all,

I am working on the genomics data and need some help with the cordinates of introns. I have a data frame of few exons(having start and end position) and i wanted to get the coordinates(start and end position) of the previous and next intron to the paticular exons.

Exon intron cordinates, cordinates of the red exons given(green) and trying to find the cordinates of the introns before and after

(the red are the exons that i have and there cordinates(marked in green), now trying to get the cordinates of the previous intron and next intron of these exons)

So, what i am trying is to get the previous and next intron cordinates of the introns. I have the gtf file (GENCODE v25.p7) and by using genomics features package have also extracted all exons and all introns from the gtf file, but unable to get the required introns.

rna-seq exons introns • 655 views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by HK40

Just a pointer: biomaRt might be a good place to begin. You can set up an EnsEMBL mart and get exon coordinates for the gene of your query exon. Once you get that data, you can pick your exon of interest, its two surrounding exons and use their end points to get neighboring introns.

If you wish to group your exons, you can do that by finding the first exon's 5' neighbor intron and the last exon's 3' neighbor intron. It'll be some math, but nothing too convoluted.

ADD REPLYlink written 2.1 years ago by RamRS27k
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