Daniel:Notebook/ComboLock/CProbeDesign: Difference between revisions

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#Must install R, Primer3, and Blast+ before using
#Must install R, Primer3, and Blast+ before using
#Make blast data
#Make blast databases;
##make one for repetitive regions (from [http://www.girinst.org/repbase/ Repbase])
makeblastdb -in repbase.fa -dbtype nucl
##Make one for transcriptome; use only high quality bases (from [ftp://ftp.ncbi.nlm.nih.gov/ NCBI ftp])
makeblastdb -in rna_human_high_qual.fa -parse_seqids -dbtype nucl
#In R:
#In R:
  library(devtools)
  library(devtools)
  install_github("nolanlab/PLAYRDesign")
  install_github("nolanlab/PLAYRDesign")
  library(PLAYRDesign)
  library(PLAYRDesign)

Revision as of 16:10, 21 April 2016

C Probe Design

Back to Notebook

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

  1. Must install R, Primer3, and Blast+ before using
  2. Make blast databases;
    1. make one for repetitive regions (from Repbase)
makeblastdb -in repbase.fa -dbtype nucl
    1. Make one for transcriptome; use only high quality bases (from NCBI ftp)
makeblastdb -in rna_human_high_qual.fa -parse_seqids -dbtype nucl
  1. In R:
library(devtools)
install_github("nolanlab/PLAYRDesign")
library(PLAYRDesign)