Daniel:Notebook/ComboLock/CProbeDesign
Jump to navigation
Jump to search
C Probe Design
This page describes the methods used for designing C-Probes for Combo Lock. The illustration below shows what a C-probe is expected to look like. The descriptions given include the original design sizes.
Designing Transcript Matching Region
- Taken from Frei et al paper
- README for probe design software
- Must install R, Primer3, and Blast+ before using
- Make blast databases
- make one for repetitive regions (from Repbase) makeblastdb -in repbase.fa -dbtype nucl
- Make one for transcriptome; use only high quality bases (from NCBI ftp) makeblastdb -in rna_human_high_qual.fa -parse_seqids -dbtype nucl
- In R: library(devtools) install_github("nolanlab/PLAYRDesign") library(PLAYRDesign)
- Next make a library from UCSC in R: library(GenomicFeatures) txdb <- makeTxDbFromUCSC(genome = "hg19", tablename = "refGene") saveDb(txdb, "PUT THE PATH TO THE OUTPUT FILE HERE")
- Finally, run PLAYRDesign
- Select a file (any file) in the working directory you wish to use
- You must have a configuartion file in the directory you wish to use (see below)
- You can hit escape any time in the R window to stop PLAYRDesign
PLAYRDesign.run()