[Bioc-devel] Known Genes replaced by GENCODE genes at UCSC

[Robert Castelo]

hi,

if i'm interpreting this correctly, the news archive of the UCSC Genome 
Browser accessible here:

  http://genome.ucsc.edu/goldenPath/newsarch.html

announced on June 29th, 2015, that they are discontinuing the generation 
of UCSC Known Genes annotations for human, and provide the Gencode 
annotations as default replacement.

the BioC site provides as default gene annotations for human the UCSC 
Known Genes track and currently does not provide the Gencode annotations.

the GenomicFeatures package allows one to build such an annotation 
package. unfortunately the current "supported" UCSC tables that can be 
easily used via 'makeTxDbPackageFromUCSC()' reports up to Gencode 
version V17:

library(GenomicFeatures)

xx <- supportedUCSCtables()
xx[grep("GENCODE Genes", xx$track), ]
                                              track subtrack
wgEncodeGencodeBasicV17          GENCODE Genes V17     <NA>
wgEncodeGencodeCompV17           GENCODE Genes V17     <NA>
wgEncodeGencodePseudoGeneV17     GENCODE Genes V17     <NA>
wgEncodeGencode2wayConsPseudoV17 GENCODE Genes V17     <NA>
wgEncodeGencodePolyaV17          GENCODE Genes V17     <NA>
wgEncodeGencodeBasicV14          GENCODE Genes V14     <NA>
wgEncodeGencodeCompV14           GENCODE Genes V14     <NA>
wgEncodeGencodePseudoGeneV14     GENCODE Genes V14     <NA>
wgEncodeGencode2wayConsPseudoV14 GENCODE Genes V14     <NA>
wgEncodeGencodePolyaV14          GENCODE Genes V14     <NA>
wgEncodeGencodeBasicV7            GENCODE Genes V7     <NA>
wgEncodeGencodeCompV7             GENCODE Genes V7     <NA>
wgEncodeGencodePseudoGeneV7       GENCODE Genes V7     <NA>
wgEncodeGencode2wayConsPseudoV7   GENCODE Genes V7     <NA>
wgEncodeGencodePolyaV7            GENCODE Genes V7     <NA>

which is about 2 years old. current Gencode gene annotations are V24 and 
at least V22 was available at:

http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database

before the last BioC release.

according to a recent announcement at the BioC support site:

https://support.bioconductor.org/p/71574

AnnotationHub seems to be now the proper way to import the most recent 
Gencode annotations into BioC. however, at least in my hands, making the 
corresponding TxDb object produces an error; see the following example:

library(AnnotationHub)

ah <- AnnotationHub()
human_gff <- query(ah, c("Gencode", "gff", "human"))

gencodeV23basicGFF <- ah[["AH49556"]]
metadata <- data.frame(name=c("Data source", "Genome", "Organism",
                               "Resource URL", "Full dataset"),
                        value=c(ah["AH49556"]$dataprovider, 
ah["AH49556"]$genome,
                                ah["AH49556"]$species, 
ah["AH49556"]$sourceurl, "no"))
txdb <- makeTxDbFromGRanges(gencodeV23basicGFF, metadata=metadata)
Error in .merge_transcript_parts(transcripts) :
   The following transcripts have multiple parts that cannot be merged 
because of incompatible seqnames: ENST00000244174.9,
   ENST00000262640.10, ENST00000286448.10, ENST00000302805.6, 
ENST00000313871.7, ENST00000326153.8, ENST00000331035.8,
   ENST00000334060.7, ENST00000334651.9, ENST00000355432.7, 
ENST00000355805.6, ENST00000359512.7, ENST00000369423.6,
   ENST00000381180.7, ENST00000381184.5, ENST00000381187.7, 
ENST00000381192.7, ENST00000381218.7, ENST00000381222.6,
   ENST00000381223.8, ENST00000381229.8, ENST00000381233.7, 
ENST00000381241.7, ENST00000381261.7, ENST00000381297.8,
   ENST00000381317.7, ENST00000381333.8, ENST00000381401.9, 
ENST00000381469.6, ENST00000381500.5, ENST00000381509.7,
   ENST00000381524.7, ENST00000381529.7, ENST00000381566.5, 
ENST00000381567.7, ENST00000381575.5, ENST00000381578.5,
   ENST00000381657.6, ENST00000381663.7, ENST00000390665.7, 
ENST00000391707.6, ENST00000399012.5, ENST00000399966.8,
   ENST00000400841.6, ENST00000411342.5, ENST00000412936


on top of this, even if it would work, these annotations are anchored at 
Ensembl Gene identifiers while the gene-centric annotations at 
org.Hs.eg.db are anchored at Entrez Gene identifiers. this means that 
more code would have to be involved to add the corresponding Entrez IDs 
(resolving multiplicities, etc.) and produce a TxDb package that can be 
used across many of the typical BioC pipelines.

since human gene annotations are at the core of many BioC pipelines, i'd 
like to suggest for the forthcoming release cycles, that the BioC core 
team packages Gencode annotations anchored at Entrez IDs, at least what 
is called the "basic set", similarly to what is done with 
TxDb.Hsapiens.UCSC.knownGene to have an easy starting point for the 
analysis of human data.


cheers,

robert.