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

2016-01-11 Thread Hervé Pagès
With GenomicFeatures 1.23.16: > txdb <- makeTxDbFromUCSC("hg38", "knownGene") Download the knownGene table ... OK Download the knownToLocusLink table ... OK Extract the 'transcripts' data frame ... OK Extract the 'splicings' data frame ... OK Download and preprocess the 'chrominfo' data frame

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

2016-01-11 Thread Robert Castelo
that looks great, thanks Hervé for addressing this quickly. robert. On 1/11/16 11:18 PM, Hervé Pagès wrote: With GenomicFeatures 1.23.16: > txdb <- makeTxDbFromUCSC("hg38", "knownGene") Download the knownGene table ... OK Download the knownToLocusLink table ... OK Extract the 'transcripts'

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

2016-01-11 Thread Rainer Johannes
Tim > Triche, Jr. > Sent: Monday, January 11, 2016 2:02 PM > To: Vincent Carey > Cc: bioc-devel@r-project.org > Subject: Re: [Bioc-devel] Known Genes replaced by GENCODE genes at UCSC > > ENSEMBL > > knownGene was always a disaster. For extra amusement/horror, be sur

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

2016-01-11 Thread Hervé Pagès
Hi Vince, Robert, On 01/11/2016 07:07 AM, Vincent Carey wrote: On Mon, Jan 11, 2016 at 9:29 AM, Robert Castelo wrote: hi, if i'm interpreting this correctly, the news archive of the UCSC Genome Browser accessible here:

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

2016-01-11 Thread Hervé Pagès
Hi Robert and others, I looked at this and the new situation doesn't seem as disruptive as it sounds. The bulk of the data for both tracks (i.e. the "UCSC Genes" track for hg19 and the "GENCODE v22" track for hg38) is stored in the knownGene table. The hg19.knownGene table is described here:

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

2016-01-11 Thread Paul Grosu
Genes replaced by GENCODE genes at UCSC ENSEMBL knownGene was always a disaster. For extra amusement/horror, be sure to check out the sad saga of the TCGA GAF and its disconnection from knownGenes as well as reality. Three cheers for rendering transcript-level estimates useless

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

2016-01-11 Thread 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

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

2016-01-11 Thread Vincent Carey
On Mon, Jan 11, 2016 at 9:29 AM, Robert Castelo wrote: > 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

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

2016-01-11 Thread Robert Castelo
hi, On 01/11/2016 04:07 PM, Vincent Carey wrote: [...] Is it true that there is an asymmetry between Entrez gene ID and Ensembl gene ID for querying org.Hs.eg.db (I tend to prefer Homo.sapiens as a symbol mapping resource)? Both ENTREZID and ENSEMBL are listed as keytypes. My question is

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

2016-01-11 Thread Vincent Carey
I think these are all good observations and we may benefit from a wider discussion on the support site? the abandonment of knownGene seems to have clear implications for changing our most visible txdb examples. what should we change to? can we make a more future-proof design for these

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

2016-01-11 Thread Tim Triche, Jr.
ENSEMBL knownGene was always a disaster. For extra amusement/horror, be sure to check out the sad saga of the TCGA GAF and its disconnection from knownGenes as well as reality. Three cheers for rendering transcript-level estimates useless (and no this was not Katie's fault) Rainer and many