Daniel:Notebook/ComboLock/CProbeDesign: Difference between revisions
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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>Must install R, Primer3, and Blast+ before using | ||
<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 | ||
<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
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.
Designing Transcript Matching Region
- Taken from Frei et al paper
- README for probe design software
- Must install R, Primer3, and Blast+ before using
- start="2">Make blast databases
- make one for repetitive regions (from Repbase) makeblastdb -in repbase.fa -dbtype nucl
- Make one for transcriptome; use only high quality bases (from NCBI ftp) makeblastdb -in rna_human_high_qual.fa -parse_seqids -dbtype nucl
- In R: library(devtools) install_github("nolanlab/PLAYRDesign") library(PLAYRDesign)