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

[zhao shilin]

Thanks Hervé!

2016-10-17 2:18 GMT-05:00 Hervé Pagès <hpages at fredhutch.org>:

> 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.knownG
>> ene,
>> 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
>>
>>         [[alternative HTML version deleted]]
>>
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>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
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> Fax:    (206) 667-1319
>

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