ucscTables() does not work properly for hs1 genome

[hpages]

Based on the online Table Browser at https://genome.ucsc.edu/cgi-bin/hgTables, the tables for track NCBI RefSeq for hs1 are: hub_3671779_ncbiRefSeq, hub_3671779_ncbiRefSeqCurated, hub_3671779_ncbiRefSeqPredicted, hub_3671779_ncbiRefSeqOther, and hub_3671779_ncbiRefSeqPsl.

However, with the latest rtracklayer (1.61.2), ucscTables() gives me:

library(rtracklayer)

ucscTables("hs1", "NCBI RefSeq")
# [1] "hub_3671779_hgUniqueHg38" "hub_3671779_hgUniquehg19"

Somethin' ain't right.

Thanks, H.

[MurliNair]

I am also having issues accessing it. library(rtracklayer) library(GenomicFeatures) library(TxDb.Mmusculus.UCSC.mm10.knownGene) mm10.refseq.db <- makeTxDbFromUCSC(genome="mm10", table="refGene")

Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie

supportedUCSCtables(genome="hg19", url="http://genome.ucsc.edu/cgi-bin/")

Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie

[hpages]

@MurliNair See issue #95 This has nothing to do with the ucscTables() issue for hs1.

[sanchit-saini]

For now, I have created a PR to fix it, though the root cause of this issue was kind of weird. ucscTableTracks() was making a request to the "https://genome-euro.ucsc.edu/" server, which was returning different results than "https://genome.ucsc.edu"

I thought the UCSC mirror pointed to the same genomic data, or am I missing something @hpages?

[hpages]

Thanks @sanchit-saini for looking into this.

I thought the UCSC mirror pointed to the same genomic data, or am I missing something @hpages?

I thought that too. Maybe @maximilianh can clarify?

Thanks

[maximilianh]

Yes. The three mirrors (ÇA, Bielefeld=Europe, Tokyo=Asia) are (should be) identical. I hope to have a China mirror soon.

They only differ in a few tracks for a few minutes per day or week, when OMIM etc are updated.

On Sat, Oct 21, 2023 at 08:27 Hervé Pagès @.***> wrote:

Thanks @sanchit-saini https://github.com/sanchit-saini for looking into this.

I thought the UCSC mirror pointed to the same genomic data, or am I missing something @hpages https://github.com/hpages?

I thought that too. Maybe @maximilianh https://github.com/maximilianh can clarify?

Thanks

— Reply to this email directly, view it on GitHub https://github.com/lawremi/rtracklayer/issues/98#issuecomment-1773691960, or unsubscribe https://github.com/notifications/unsubscribe-auth/AACL4TIAHO3WNJWTZA2WXZTYANTNXAVCNFSM6AAAAAA6JNPR42VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTONZTGY4TCOJWGA . You are receiving this because you were mentioned.Message ID: @.***>

[jennyujin22]

Hello, I got an issue about Ucsc track, which is related to #99

When I learn the code

rTrack <- Gviz::UcscTrack(genome="hg19", chromosome=chrom, track = "NCBI RefSeq", table = "ncbiRefSeq", from=minbase, to=maxbase, trackType="GeneRegionTrack", rstarts="exonStarts", rends="exonEnds", gene="name", symbol="name2", transcript="name", strand="strand", fill="darkblue",stacking="squish", name="RefSeq", showId=TRUE, geneSymbol=TRUE)

I got an error

**

"Error in normArgTrack(track, trackids) : Unknown track: refSeqComposite"

**

When I did trace back, I thought that the error was more likely related to rtracklayer's ucsc.R (I found the function normArgTrack in this script) than Gviz, which supplied the UcscTrack I used.

PS: When I looked up the table names for NCBI RefSeq, I got the lists.

ucscTables("hg19", "NCBI RefSeq")

[1] "ncbiRefSeq" "ncbiRefSeqCurated"
[3] "ncbiRefSeqOther" "ncbiRefSeqPsl"
[5] "ncbiRefSeqGenomicDiff" "refGene"
[7] "ncbiRefSeqSelect" "ncbiRefSeqHgmd"
[9] "all_est" "all_mrna"
[11] "ccdsInfo" "hgFixed.gbCdnaInfo"
[13] "hgFixed.gbMiscDiff" "hgFixed.gbSeq"
[15] "hgFixed.gbWarn" "hgFixed.imageClone"
[17] "hgFixed.refLink" "hgFixed.refSeqStatus"
[19] "hgFixed.refSeqSummary" "kgXref"
[21] "knownToRefSeq" "mrnaOrientInfo"
[23] "ncbiRefSeqCds" "ncbiRefSeqLink"
[25] "refFlat" "refSeqAli"
[27] "seqNcbiRefSeq" "ucscRetroInfo5"
[29] "wgEncodeGencodeRefSeqV24lift37" "wgEncodeGencodeRefSeqV27lift37" [31] "wgEncodeGencodeRefSeqV28lift37" "wgEncodeGencodeRefSeqV31lift37" [33] "wgEncodeGencodeRefSeqV33lift37" "wgEncodeGencodeRefSeqV34lift37" [35] "wgEncodeGencodeRefSeqV35lift37" "wgEncodeGencodeRefSeqV36lift37" [37] "wgEncodeGencodeRefSeqV37lift37" "wgEncodeGencodeRefSeqV38lift37" [39] "wgEncodeGencodeRefSeqV39lift37" "wgEncodeGencodeRefSeqV40lift37" [41] "wgEncodeGencodeRefSeqV41lift37" "wgEncodeGencodeRefSeqV42lift37" [43] "wgEncodeGencodeRefSeqV43lift37" "wgEncodeGencodeRefSeqV44lift37" [45] "xenoEst" "xenoMrna"
[47] "xenoRefGene" "xenoRefSeqAli"

That's why I entered 'ncbiRefSeq' for the table value.

Could anyone give some information about the error?

Many thanks,

Sincerely,

Yujin Kim.