I am trying to retrieve exonic-intronic locations and sequences using biomaRt. Basically, I want to retrieve the sequence->exons tab on ensembl BUT FOR A TRANSCRIPT LIST-QUERY
Thus, I tried to run this code to retrieve exon and intron list to my ensembl transcript list (enstxxxxXXX)
human <- useDataset( "hsapiens_gene_ensembl", mart = useMart( "ensembl" ) ) mart = useMart("ENSEMBL_MART_ENSEMBL",dataset="hsapiens_gene_ensembl", host="www.ensembl.org") getSequence(id = ensdf, type="ensembl_transcript_id ", seqType="transcript_exon_intron", upstream=100, mart=ensembl)
However, it gives an error like:
> Error in martCheck(mart, c("ensembl", "ENSEMBL_MART_ENSEMBL")) : No dataset selected, please select a dataset first. You can see the available datasets by using the listDatasets function see ?listDatasets for more information. Then you should create the Mart object by using the useMart function. See ?useMart for more information
Do you know how to solve this error? Or another way to retrieve intronic locations and sequences?
Thank you so much!