Question

the coordinates of exons of RefSeq or ENSEMBL genes

0

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Bogdan ▴ 670

@bogdan-2367

Last seen 6 months ago

Palo Alto, CA, USA

Dear all,

please may i ask a simple question :

in BioC, what is the simplest (or the most direct way) to retrieve the COORDINATES of EXONS for RefSeq or ENSEMBL genes ?

thanks a lot,

-- bogdan

txdb genome exons • 2.6k views

ADD COMMENT • link updated 4.7 years ago by Martin Morgan 25k • written 4.7 years ago by Bogdan ▴ 670

score 3 · Accepted Answer · 2019-08-01

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Wei Shi ★ 3.6k

@wei-shi-2183

Last seen 10 days ago

Australia/Melbourne/Olivia Newton-John …

You can certainly use Bioc core packages to do so, but the getInBuiltAnnotation function in Rsubread offers you a simple way to get this information for human and mouse RefSeq genes.

ADD COMMENT • link 4.7 years ago Wei Shi ★ 3.6k

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thanks a lot, Wei ! looking at the example that you did provide, it works great :

 x <- getInBuiltAnnotation("hg38")
 x[1:5,]

ADD REPLY • link 4.7 years ago Bogdan ▴ 670

score 3 · Accepted Answer · 2019-08-02

For ensembl, load the ensembldb and AnnotationHub and query for EnsDb objects for Homo sapiens, release 97

> library(ensembldb)
> library(AnnotationHub)
> hub = AnnotationHub()
snapshotDate(): 2019-07-10
> query(hub, c("EnsDb", "Homo sapiens", "97"))

This returns a single record with id AH73881. Retrieve and use exons() to extract the information

> exons(hub[["AH73881"]])
downloading 0 resources
loading from cache
GRanges object with 828532 ranges and 1 metadata column:
                  seqnames            ranges strand |         exon_id
                     <Rle>         <IRanges>  <Rle> |     <character>
  ENSE00002234944        1       11869-12227      + | ENSE00002234944
  ENSE00001948541        1       12010-12057      + | ENSE00001948541
  ENSE00001671638        1       12179-12227      + | ENSE00001671638
  ENSE00003582793        1       12613-12721      + | ENSE00003582793
  ENSE00001758273        1       12613-12697      + | ENSE00001758273
              ...      ...               ...    ... .             ...
  ENSE00001741452        Y 26628271-26628437      - | ENSE00001741452
  ENSE00001681574        Y 26630647-26630749      - | ENSE00001681574
  ENSE00001638296        Y 26633345-26633431      - | ENSE00001638296
  ENSE00001797328        Y 26634523-26634652      - | ENSE00001797328
  ENSE00001794473        Y 56855244-56855488      + | ENSE00001794473
  -------
  seqinfo: 424 sequences from GRCh38 genome

Use identical steps for refSeq (knownGene) annotations, using

query(hub, c("TxDb", "Homo sapiens"))