Daniel:Notebook/ComboLock/CProbeDesign

From ZhangLabWiki
Jump to navigation Jump to search

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)