Daniel:Notebook/ComboLock/CProbeDesign: Difference between revisions

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<ol>Must install R, Primer3, and Blast+ before using
<ol>Must install R, Primer3, and Blast+ before using
<li> start="2">Make blast databases</li>
<li>Make blast databases</li>
<li>make one for repetitive regions (from [http://www.girinst.org/repbase/ Repbase])</li>
<li>make one for repetitive regions (from [http://www.girinst.org/repbase/ Repbase])</li>
  makeblastdb -in repbase.fa -dbtype nucl
  makeblastdb -in repbase.fa -dbtype nucl

Revision as of 16:15, 21 April 2016

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)