makeTranscriptDbFromUCSC 'refLink' table error
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cmarcone • 0
@cmarcone-11476
Last seen 7.5 years ago

Hello,

I am receiving an error when trying to build a transcript database using the makeTranscriptDbFromUCSC command. Specifically, when I input the paramaters for hg38 as so:

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hg38.tx<-makeTranscriptDbFromUCSC(genome="hg38", tablename="refGene")

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I am able to download the refGene table, but then receive the following error:

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Download the refGene table . . . OK

Download the refLink table . . . Error in normArgTable(value, x) : unknown table name 'refLink'

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Upon looking on the hg38 genome browser it appears that the refLink table is still connected to the refGene table in hg38 ( I checked in the table browser), as one would assume it should be, so I don't know why I'm getting this error. 

If there is a work around I would appreciate knowing it, Thank you.

 

annotation • 996 views
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Answered. I was able to develop a work around using a different package.

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caldavis • 0
@caldavis-11479
Last seen 7.5 years ago

Some tables do not change with each assembly, including refLink. UCSC moved these 'fixed' tables to a new area starting mid-June, 2016. See https://genome.ucsc.edu/FAQ/FAQdownloads#download35

hth, --Caleb

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Thank you Caleb. I was able to get the preformatted transcript database using TxDb.Hsapiens.UCSC.hg38.knownGene.

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