[Bioc-devel] how to get genomic sequences?
Roger Liu wrote:
Hi, I have a set of data with chromosome number and coordinates of the sequences such as,chr10, start 1000, end 2000. I have tried using biomart to retrieve the genomic sequences for my dataset, but I didn't get success, I used seqType argument as: seqType="genomic", it reported error as"The type of sequence specified with seqType is not available. Please select from: cdna, peptide, 3utr, 5utr", but I have seen this "genomic" argument for seqType in the help file. So what's going on there? Or anyone can recommend a package which can help me retrieve the genomic sequences from hg18 with known chromosome number and sequences coordinates(start and end).
URLs like so: http://genome.ucsc.edu/cgi-bin/das/hg18/dna?segment=chr1:1000,2000;segment=chr2:1000,2000 will get you sequences of interest. These come as simple well-formed XML, so you can use the XML package to parse them pretty easily. You can do one-at-a-time, or string together a bunch. Sean