Daniel:Notebook/ComboLock/CProbeDesign: Difference between revisions
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install_github("nolanlab/PLAYRDesign") | install_github("nolanlab/PLAYRDesign") | ||
library(PLAYRDesign) | library(PLAYRDesign) | ||
<li>Next make a library from UCSC in R:</li> | |||
library(GenomicFeatures) | |||
txdb <- makeTxDbFromUCSC(genome = "hg19", tablename = "refGene") | |||
saveDb(txdb, "PUT THE PATH TO THE OUTPUT FILE HERE") | |||
<li>Finally, run PLAYRDesign | |||
<ol type="A"> | |||
<li>Select a file (any file) in the working directory you wish to use</li> | |||
<li>You must have a configuartion file in the directory you wish to use (see below)</li> | |||
<li>You can hit escape any time in the R window to stop PLAYRDesign</li></ol> | |||
</li> | |||
PLAYRDesign.run() | |||
</ol> | </ol> |
Revision as of 16:22, 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
- 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)
- Next make a library from UCSC in R: library(GenomicFeatures) txdb <- makeTxDbFromUCSC(genome = "hg19", tablename = "refGene") saveDb(txdb, "PUT THE PATH TO THE OUTPUT FILE HERE")
- Finally, run PLAYRDesign
- Select a file (any file) in the working directory you wish to use
- You must have a configuartion file in the directory you wish to use (see below)
- You can hit escape any time in the R window to stop PLAYRDesign
PLAYRDesign.run()