sppDesigner is a software for designing padlock probes for in situ profiling. It is based on ppDesginer from Diep et al. Nature Methods (2012).
- Perl interpreter which is preinstalled on many linux systems.
- SortArray package on perl
sudo perl -MCPAN -e shell
install Sort::Array
- a reference genome with one fasta file per chromosome
To call ppDesigner you need two files 1) a file specifying regions on the reference genome for which you want to target with padlock probes, 2) a "job file" with all the settings. We have included an example run with t1.target as the target file, "j1.jfile" as the job file. "run_ppd.sh" runs ppDesigner and creates the output "testrun.ppd".
The notebook "run_sppd.ipynb" runs sppDesigner for all genes in the genome and creates a resource from which probes can be pulled for every new probe set. To run that, you need a genome annotation .gtf file (Gencode or RefSeq), BWA aligner, with a BWA genome index.
sppDesigner is a modified version of ppDesigner (PMID: 22306810). The original software is covered by a copyright owned by UC San Diego (invent@ucsd.edu)