[Bioc-devel] A bug in TxDb.Hsapiens.UCSC.hg38.knownGene?

[Hervé Pagès]

Hi Shilin,

I answered this on the support site:

   https://support.bioconductor.org/p/88232/#88347

Cheers,
H.

On 10/16/2016 08:35 PM, zhao shilin wrote:
> Dear BioC team,
>
> I think I found something incorrect in  TxDb.Hsapiens.UCSC.hg38.knownGene,
> and reported in https://support.bioconductor.org/p/88232/ but didn't get
> reply. I think it is a bug, so decided to send it via email to let you know.
>
> I am using the developing version of TxDb.Hsapiens.UCSC.hg38.knownGene,
> because the release version is build in 2015 and has a lot of difference
> with UCSC website. Here is the R code for the bug:
>
> require(TxDb.Hsapiens.UCSC.hg38.knownGene)
> require(GenomicRanges)
>
> geneDb=TxDb.Hsapiens.UCSC.hg38.knownGene
> allGeneRange<-genes(geneDb)
> allGeneRange["875"]
> txs <- transcriptsBy(TxDb.Hsapiens.UCSC.hg38.knownGene)
> txs["875"]
>
>
> We can find CBS gene (txs["875"]) has 25 transcripts, from two
> regions: chr21   [6444869, 6467509] and chr21 [43075107, 43076288]
>
> 1. CBS gene ("875") was only in chr21 [43075107, 43076288]. The region
> of chr21   [6444869, 6467509] was CBSL gene ("102724560"). But CBSL was not
> in the database, and its transcripts were recorded in CBS.
>
> 2. The gene region of CBS gene (allGeneRange["875"]) was in chr21 [6444869,
> 43076943], which included all the region between 6444869-43076943. But it
> is not correct as they were two separate regions.
>
>
> Thanks!
>
> Shilin
>
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>
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-- 
Hervé Pagès

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