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


#Must install R, Primer3, and Blast+ before using
<ol>Must install R, Primer3, and Blast+ before using</ol>
#Make blast databases;
<ol start="2">Make blast databases
##make one for repetitive regions (from [http://www.girinst.org/repbase/ Repbase])
<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
##Make one for transcriptome; use only high quality bases (from [ftp://ftp.ncbi.nlm.nih.gov/ NCBI ftp])
<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:
#In R:

Revision as of 16:14, 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
    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)