I am looking for a way to retrieve DNA sequences from Ensembl May 2017 archive, based on coordinates. I thought using Biomart package would be useful for getting DNA sequences, however, it did not work. Apparently, sequence type (seqType, type) is required for obtaining a sequence using getSequence function.
ensembl<-useMart(host="may2017.archive.ensembl.org", biomart="ENSEMBL_MART_ENSEMBL", dataset="hsapiens_gene_ensembl") seq<-biomaRt::getSequence(chromosome="X", start = 100639991, end = 100644991 , mart=ensembl )
This gives the following error:
Error in biomaRt::getSequence(chromosome = "X", start = 100639991, end = 100644991, : Please specify the type of sequence that needs to be retrieved when using biomaRt in web service mode. Choose either gene_exon, transcript_exon,transcript_exon_intron, gene_exon_intron, cdna, coding,coding_transcript_flank,coding_gene_flank,transcript_flank,gene_flank,peptide, 3utr or 5utr
Is there a nice way for getting the DNA sequences of a large list of genomic coordinates?
Thank you very much.