Hi Nico, thanks for the hint. I will have a look at AnnotationHub. I was looking for the transcript_biotype rather than the gene_biotype (to discriminate protein_coding isoforms from the rest like processed_transcript etc), but this should also be included in the Ensembl gtf file. Thanks, Kathi On 16/11/13 22:39, Nicolas Delhomme wrote: > Hej Kathi! > > In a different thread (GTF file error when using easyRNAseq), Martin mentioned that you can access ensemble gff files through AnnotationHub. I just copy part of this answer below and as you can see, the gene_biotype is part of the annotation: > >> library(AnnotationHub) >> hub = AnnotationHub() >> hub$ensembl.release.73.<tab> > hub$ensembl.release.73.fasta. ... [378] > hub$ensembl.release.73.gtf. ... [63] >> xx = hub$ensembl.release.73.gtf.gallus_gallus.Gallus_gallus.Galgal4 .73.gtf_0.0.1.RData >> xx > GRanges with 381368 ranges and 12 metadata columns: > seqnames ranges strand | source type > <rle> <iranges> <rle> | <factor> <factor> > [1] 1 [1735, 2449] + | protein_coding exon > [2] 1 [2379, 2449] + | protein_coding CDS > score phase gene_id transcript_id > <numeric> <integer> <character> <character> > [1] <na> <na> ENSGALG00000009771 ENSGALT00000015891 > [2] <na> 0 ENSGALG00000009771 ENSGALT00000015891 > exon_number gene_biotype exon_id protein_id > <numeric> <character> <character> <character> > [1] 1 protein_coding ENSGALE00000301221 <na> > [2] 1 protein_coding <na> ENSGALP00000015874 > gene_name transcript_name > <character> <character> > [1] <na> <na> > [2] <na> <na> > [ reached getOption("max.print") -- omitted 9 rows ] > --- > seqlengths: > 1 2 ... AADN03010940.1 > NA NA ? NA > > Hope this helps, > > Cheers, > > Nico > > --------------------------------------------------------------- > Nicolas Delhomme > > Genome Biology Computational Support > > European Molecular Biology Laboratory > > Tel: +49 6221 387 8310 > Email: nicolas.delhomme at embl.de > Meyerhofstrasse 1 - Postfach 10.2209 > 69102 Heidelberg, Germany > --------------------------------------------------------------- > > > > > > On 7 Nov 2013, at 14:11, Kathi Zarnack <zarnack at="" ebi.ac.uk=""> wrote: > >> Hi, >> >> I wanted to ask whether any of the annotation packages contains information on the transcript biotype (protein-coding, etc). I would like to select only protein-coding isoforms from Ensembl annotation, but I could not find any package that includes this information (otherwise I will get it with biomaRt, I just wondered whether it is already included somewhere). >> >> Also, I tried to download GENCODE annotation using GenomicFeatures, and got the following error: >> >>> test=makeTranscriptDbFromUCSC(genome="hg19", tablename="wgEncodeGencodeManualV3") >> Error in tableNames(ucscTableQuery(session, track = track)) : >> error in evaluating the argument 'object' in selecting a method for function 'tableNames': Error in normArgTrack(track, trackids) : Unknown track: Gencode Genes >> >> I tried to get the same table for hg18, but I get only one step further: >> >> test=makeTranscriptDbFromUCSC(genome="hg18", tablename="wgEncodeGencodeManualV3") >> Download the wgEncodeGencodeManualV3 table ... OK >> Download the wgEncodeGencodeClassesV3 table ... Error in normArgTable(value, x) : >> unknown table name 'wgEncodeGencodeClassesV3' >> >> Thank you very much for your help, >> Kathi >> >> >> ------------------------------------------ >> >>> sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 >> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] GenomicFeatures_1.14.0 AnnotationDbi_1.24.0 Biobase_2.22.0 >> [4] GenomicRanges_1.14.3 XVector_0.2.0 IRanges_1.20.5 >> [7] BiocGenerics_0.8.0 BiocInstaller_1.12.0 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.18.0 Biostrings_2.30.0 bitops_1.0-6 BSgenome_1.30.0 >> [5] DBI_0.2-7 RCurl_1.95-4.1 Rsamtools_1.14.1 RSQLite_0.11.4 >> [9] rtracklayer_1.22.0 stats4_3.0.2 tcltk_3.0.2 tools_3.0.2 >> [13] XML_3.98-1.1 zlibbioc_1.8.0 >> >> >> -- >> Dr. Kathi Zarnack >> Luscombe Group >> >> European Molecular Biology Laboratory >> European Bioinformatics Institute (EMBL-EBI) >> Wellcome Trust Genome Campus >> Hinxton >> Cambridge CB10 1SD >> United Kingdom >> >> emailzarnack at ebi.ac.uk >> tel +44 1223 494 526 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Dr. Kathi Zarnack Luscombe Group European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom email zarnack at ebi.ac.uk tel +44 1223 494 526

Hi Herve, thanks for pointing me to the files and also for updating GenomicFeatures. It's a great package! I let you know if I run into any other problems. Best regards, Kathi On 17/11/13 21:43, Hervé Pagès wrote: > Hi Kathi, > > On 11/07/2013 05:11 AM, Kathi Zarnack wrote: >> Hi, >> >> I wanted to ask whether any of the annotation packages contains >> information on the transcript biotype (protein-coding, etc). I would >> like to select only protein-coding isoforms from Ensembl annotation, but >> I could not find any package that includes this information (otherwise I >> will get it with biomaRt, I just wondered whether it is already included >> somewhere). >> >> Also, I tried to download GENCODE annotation using GenomicFeatures, and >> got the following error: >> >> > test=makeTranscriptDbFromUCSC(genome="hg19", >> tablename="wgEncodeGencodeManualV3") >> Error in tableNames(ucscTableQuery(session, track = track)) : >> error in evaluating the argument 'object' in selecting a method for >> function 'tableNames': Error in normArgTrack(track, trackids) : Unknown >> track: Gencode Genes >> >> I tried to get the same table for hg18, but I get only one step further: >> >> test=makeTranscriptDbFromUCSC(genome="hg18", >> tablename="wgEncodeGencodeManualV3") >> Download the wgEncodeGencodeManualV3 table ... OK >> Download the wgEncodeGencodeClassesV3 table ... Error in >> normArgTable(value, x) : >> unknown table name 'wgEncodeGencodeClassesV3' > > Note that the wgEncodeGencodeManualV3 table seems to be for hg18 > only: there doesn't seem to be such table for hg19. > > For hg19, UCSC provides 3 GENCODE tracks: GENCODE Genes V17, GENCODE > Genes V14, and GENCODE Genes V7. Each of them contains 5 tables > that are compatible with makeTranscriptDbFromUCSC(). For example, > for GENCODE Genes V17, those tables are: > > wgEncodeGencodeBasicV17 > wgEncodeGencodeCompV17 > wgEncodeGencodePseudoGeneV17 > wgEncodeGencode2wayConsPseudoV17 > wgEncodeGencodePolyaV17 > > See here for the details: > > http://genome.ucsc.edu/cgi- bin/hgTrackUi?db=hg19&g=wgEncodeGencodeSuper > > I just made some adjustments to the GenomicFeatures package so > makeTranscriptDbFromUCSC() can work on those tables. Unfortunately > I also needed to fix support for the wgEncodeGencode*V3 tables (for > hg18) which was broken due to changes on the UCSC side. > > Those updates are in GenomicFeatures 1.14.2 (release) and 1.15.4 > (devel). Both should become available via biocLite() in the next 24 > hours or so. > > Please let us know if you run into any other problem with the > GenomicFeatures package. > > Thanks, > H. > > >> >> Thank you very much for your help, >> Kathi >> >> >> ------------------------------------------ >> >> > sessionInfo() >> R version 3.0.2 (2013-09-25) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 >> [7] LC_PAPER=en_GB.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] GenomicFeatures_1.14.0 AnnotationDbi_1.24.0 Biobase_2.22.0 >> [4] GenomicRanges_1.14.3 XVector_0.2.0 IRanges_1.20.5 >> [7] BiocGenerics_0.8.0 BiocInstaller_1.12.0 >> >> loaded via a namespace (and not attached): >> [1] biomaRt_2.18.0 Biostrings_2.30.0 bitops_1.0-6 BSgenome_1.30.0 >> [5] DBI_0.2-7 RCurl_1.95-4.1 Rsamtools_1.14.1 >> RSQLite_0.11.4 >> [9] rtracklayer_1.22.0 stats4_3.0.2 tcltk_3.0.2 tools_3.0.2 >> [13] XML_3.98-1.1 zlibbioc_1.8.0 >> >> > -- Dr. Kathi Zarnack Luscombe Group European Molecular Biology Laboratory European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD United Kingdom email zarnack at ebi.ac.uk tel +44 1223 494 526