Daniel:Notebook/ComboLock/CProbeDesign: Difference between revisions

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>Djacobse
>Djacobse
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*[https://github.com/nolanlab/PLAYRDesign/blob/master/README.md README] for probe design software
*[https://github.com/nolanlab/PLAYRDesign/blob/master/README.md README] for probe design software


<ol>Must install R, Primer3, and Blast+ before using</ol>
<ol>Must install R, Primer3, and Blast+ before using
<ol start="2">Make blast databases
<li> start="2">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
<li>Make one for transcriptome; use only high quality bases (from [ftp://ftp.ncbi.nlm.nih.gov/ NCBI ftp])</li>
<li>Make one for transcriptome; use only high quality bases (from [ftp://ftp.ncbi.nlm.nih.gov/ NCBI ftp])</li>
  makeblastdb -in rna_human_high_qual.fa -parse_seqids -dbtype nucl
  makeblastdb -in rna_human_high_qual.fa -parse_seqids -dbtype nucl
#In R:
<li>In R:</li>
  library(devtools)
  library(devtools)
  install_github("nolanlab/PLAYRDesign")
  install_github("nolanlab/PLAYRDesign")
  library(PLAYRDesign)
  library(PLAYRDesign)

Revision as of 16:15, 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

    Must install R, Primer3, and Blast+ before using
  1. start="2">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)