[Bioc-devel] Question: error in makeTxDbFromUCSC

[陈施航]

Hi GenomicFeatures support,

I am Shihang Chen, a phD student at the University of Tokyo, using
GenomicFeatures for ChIPSeeker.
I run into a problem when I was using makeTxDbFromUCSC, and really need
your help.

After I run
txdb=makeTxDbFromUCSC(genome="hg19",tablename="refGene")
I got this error.
Download the refGene table ... OK
Download the hgFixed.refLink table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Prepare the 'metadata' data frame ... OK
*Make the TxDb object ... Error in .check_foreign_key(transcripts_tx_chrom,
NA, "transcripts$tx_chrom",  : *
*  all the values in 'transcripts$tx_chrom' must be present in
'chrominfo$chrom'*

I consider the problem is that refGene version was upgraded last
November,however, GenomicFeatures haven't done corresponding changes to the
new refGene release.
I attached my survey report in this email.
If you have any clues why this is happening, please let me know.
Your help is much appreciated.
Thank you so much!

Shihang Chen