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
    Make blast databases
  1. make one for repetitive regions (from Repbase)
  2. makeblastdb -in repbase.fa -dbtype nucl
  3. Make one for transcriptome; use only high quality bases (from NCBI ftp)
  4. makeblastdb -in rna_human_high_qual.fa -parse_seqids -dbtype nucl
    1. In R:
    library(devtools) install_github("nolanlab/PLAYRDesign") library(PLAYRDesign)