Daniel:Notebook/ComboLock/CProbeDesign

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C Probe Design

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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.

File:C Probes.png

Designing Transcript Matching Region

    Must install R, Primer3, and Blast+ before using
  1. Make blast databases
  2. make one for repetitive regions (from Repbase)
  3. makeblastdb -in repbase.fa -dbtype nucl
  4. Make one for transcriptome; use only high quality bases (from NCBI ftp)
  5. makeblastdb -in rna_human_high_qual.fa -parse_seqids -dbtype nucl
  6. In R:
  7. library(devtools) install_github("nolanlab/PLAYRDesign") library(PLAYRDesign)
  8. Next make a library from UCSC in R:
  9. library(GenomicFeatures) txdb <- makeTxDbFromUCSC(genome = "hg19", tablename = "refGene") saveDb(txdb, "PUT THE PATH TO THE OUTPUT FILE HERE")
  10. Finally, run PLAYRDesign
    1. Select a file (any file) in the working directory you wish to use
    2. You must have a configuartion file in the directory you wish to use (see below)
    3. You can hit escape any time in the R window to stop PLAYRDesign
  11. PLAYRDesign.run()