Question: Chromosome Location (chrX:123456) to Genomic Feature (Exon/Intron/UTR)
0
gravatar for utkarshkapoor87
2.5 years ago by
utkarshkapoor870 wrote:

Hi Guys,

As an example: chr11:96815339

I want to find out where this site in the gene is: Exon/Intron/UTR. How can I do this?

Of course, I can use UCSC Genome Browser for a site. But if I have a huge RNA-Seq data set with these sites and I want the information of their location, how can I automate this? Any tools that you could suggest? Idea is to get a distribution of all the called locations and map them to their genic location.

Thanks,

Utkarsh

genome gene • 924 views
ADD COMMENTlink modified 16 months ago by Biostar ♦♦ 20 • written 2.5 years ago by utkarshkapoor870
0
gravatar for geek_y
2.5 years ago by
geek_y9.6k
Barcelona/CRG/London/Imperial
geek_y9.6k wrote:

Homer annotatePeaks.pl. See the section "Genomic Annotation"

Here the peak could be simply chr11 96815339 96815340

Check whether homer is based on 0 or 1 based coordinates and use the coordinates appropriately, either chr11 96815339 96815340 or chr11 96815338 96815339

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by geek_y9.6k
0
gravatar for d-cameron
2.5 years ago by
d-cameron2.0k
Australia
d-cameron2.0k wrote:

Many RNA-Seq analysis pipelines use BioConductor packages (eg DESeq2/EdgeR) so unless you're doing your lookup on a per-read bases, I would recommend starting there. The following link gives a good overview of BioConductor annotation workflows:

https://www.bioconductor.org/help/workflows/annotation/Annotation_Resources/

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by d-cameron2.0k
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