Download Zipped File
All coordinates are in GFF format (chromosome starts at base 1, interval includes end coordinate). If you have a large set of genomic regions you wish to capture, we recommend that you download these files and use BEDtools to extract the appropriate oligonucleotide sequences. You can do this using the following steps:
- Download and unzip the oligo files for the chromosome(s) of interest.
- Convert the downloaded file to GFF or BED format for use with BEDtools.
- Download and install BEDTools (v. 0.1.12+) as described on the BEDtools site
- Format a set of intervals of interest as a GFF file or a BED file. Bed format is preferable because only the chromosome, start, and end fields are required.
- Run the BEDtools intersectBed command to find the oligonucleotides that capture regions the target regions:
intersectBed -u -a oligofile.gff -b target_intervals.bed >oligos_in_intervals.gff
The file oligofile.gff is the GFF formatted file containing all the downloaded oligo information, target_intervals.bed (or .gff) is the set of target regions, and oligos_in_intervals.gff is the output from the program. If you want to capture regions from multiple chromosomes, you can either combine the downloaded files or run the command on each downloaded file separately.