biomaRt query ??
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Tim Smith ★ 1.1k
@tim-smith-1532
Last seen 7.9 years ago
Hi, I wanted to determine the locations for all the alternative splicing sites. I've made the query in biomaRt, but am not sure if this is giving me what I want. Any help would be appreciated! ##### library(biomaRt) ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") atb2 <- c("dbass5_id","dbass5_name",'hgnc_symbol','chromosome_name','s tart_position','end_position','strand') splice.locs <- getBM(attributes=atb2, mart=ensembl) print(splice.locs[1:5,]) #### thanks! [[alternative HTML version deleted]]
biomaRt biomaRt • 829 views
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@rhoda-kinsella-3200
Last seen 7.9 years ago
Hi Tim As you are only asking for the DBASS5 name and id, you will only get the aberrant 5' splice sites generated as a result of disease-causing mutations in human genes (see here for more information: http://www.som.soton.ac.uk/research/geneticsdiv/dbass5/) . You should take a look at the transcript event attributes from the Ensembl BioMart (see here for paper about this project: http://www.ncbi.nlm.nih.gov/pubmed/18978772) as this will give you the alternative splice site data i think you are looking for. <query virtualschemaname="default" formatter="TSV" header="0" uniquerows="0" count="" datasetconfigversion="0.6"> <dataset name="hsapiens_gene_ensembl" interface="default"> <attribute name="ensembl_gene_id"/> <attribute name="ensembl_transcript_id"/> <attribute name="ensembl_peptide_id"/> <attribute name="name_1078"/> <attribute name="splicing_event__dm_name_1059"/> <attribute name="splicing_event_type"/> <attribute name="name_106"/> <attribute name="seq_region_start_1078"/> <attribute name="seq_region_end_1078"/> <attribute name="seq_region_strand_1078"/> </dataset> </query> I hope that helps Regards Rhoda On 24 Oct 2011, at 20:10, Tim Smith wrote: > Hi, > > I wanted to determine the locations for all the alternative splicing > sites. I've made the query in biomaRt, but am not sure if this is > giving me what I want. Any help would be appreciated! > > ##### > library(biomaRt) > ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl") > atb2 <- > c > ("dbass5_id > ","dbass5_name > ",'hgnc_symbol > ','chromosome_name','start_position','end_position','strand') > splice.locs <- getBM(attributes=atb2, mart=ensembl) > print(splice.locs[1:5,]) > > #### > > thanks! > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 Rhoda Kinsella Ph.D. Ensembl Production Project Leader, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD, UK.
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