The OS-Seq_scripts.zip contains 2 required folders (lowercase):
The “inputs” folder should contain a tab delimited txt-file named “coordinates_to_extract.txt” with 4 columns (no header) :
- Column 1: a unique identifier for the target
- Column 2: The chromosome number, accepted values are 1 through 24 and X or Y (capitalized) (do not add chr)
- Column 3: start position of target region of interest (0-based)
- Column 4: end position of target region of interest (1-based)
The target regions will be increased in size by 500 bases to find optimal positions for the primer probes.
The “scripts” folder should contain the matlab script “os_seq_design_from_coordinates_v3.1.m”:
- Adapt the script to point to the KMER folder containing the unzipped kmer.txt files in line 23.
From within the scripts folder, run the following command to find optimally placed primer probes in the listed target regions:
nohup nice time matlab -nodisplay -nodesktop -nojvm -nosplash osseq.log 2>&1 &