How long does getCDS takes to retrieve CDS tables from UCSC

Question

[nikkihathi]

Hello!

I am using a Bioconductor package called spliceR to identify any alternative splicing events in two samples. For this purpose, I am following the basic steps suggested in the paper.

for CDS annotation I am downloaded

library(BSgenome.Hsapiens.UCSC.hg19)
require("BSgenome.Hsapiens.UCSC.hg19",character.only=T)
ucscCDS <- getCDS(selectedGenome = "hg19",repoName = "UCSC") ## Retrieving CDS tables for UCSC...

It has been more than 24 hours but the retrieving CDS tables step is still running. I am uncertain if this problem is related to the system or to the repository.

Any suggestion?

[EagleEye]

Through UCSC browser takes considerably less time,

A: I need to download a list of all human genes with their respective Esemble gene

[GenoMax]

But the original question is about retrieving this information via R.

[EagleEye]

Sorry, I just saw the title. My fault :-(

[GenoMax]

No problem. Moved to a comment. Still useful information.

Answer 1

[Giovanni M Dall'Olio]

You may have some proxy issue. Is the $http_proxy variable set?

You can also get the CDS coordinates from the Homo.sapiens package:

> biocLite(Homo.sapiens)
> library(Homo.sapiens)
> cds(TxDb.Hsapiens.UCSC.hg19.knownGene)
GRanges object with 237533 ranges and 1 metadata column:
                 seqnames           ranges strand |    cds_id
                    <Rle>        <IRanges>  <Rle> | <integer>
       [1]           chr1 [ 12190,  12227]      + |         1
       [2]           chr1 [ 12595,  12721]      + |         2
       [3]           chr1 [ 13403,  13639]      + |         3
       [4]           chr1 [ 69091,  70008]      + |         4
       [5]           chr1 [324343, 324345]      + |         5
       ...            ...              ...    ... .       ...
  [237529] chrUn_gl000228   [30530, 31035]      - |    237529
  [237530] chrUn_gl000228   [31353, 31430]      - |    237530
  [237531] chrUn_gl000228   [31660, 31734]      - |    237531
  [237532] chrUn_gl000228   [31660, 31737]      - |    237532
  [237533] chrUn_gl000228   [31996, 32173]      - |    237533
  -------
  seqinfo: 93 sequences (1 circular) from hg19 genome

The coordinates come from the same place, the UCSC repo.