Entering edit mode
Hi,
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.
For example:
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.
Did you check the documentation? Sequence type
genomicis one of the allowed options.biomaRt v2.32.1 is installed which does not allow "genomic" as the seqType. If I try I get the following:
Tagging: Mike Smith to see if he can help.