Daniel:Notebook/ComboLock/CProbeDesign: Difference between revisions
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I have attached a sample of the output probes from the C-probe designer: [[Media:C_Probe_Analysis_SOD1_VIM.pdf|C Probe Analysis SOD1/VIM (pdf)]] | I have attached a sample of the output probes from the C-probe designer: [[Media:C_Probe_Analysis_SOD1_VIM.pdf|C Probe Analysis SOD1/VIM (pdf)]] | ||
[[ | [[Media:C_Probe_Analysis_SOD1_VIM.docx|C Probe Analysis SOD1/VIM (docx)]] |
Revision as of 16:36, 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()
PLAYRDesign Configuration File
Needed to run PLAYRDesign. The name of the file must be playrdesign_conf.txt and must be in your working directory. An example is below. Note that if there are any spaces in your file (including after the path name) PLAYRDesign will not work properly
BLASTN_EXEC=/usr/bin/blastn (The full path to the blastn executable) BLASTN_DB=/opt/BLAST/ (The directory containing your BLAST database files) PRIMER3_EXEC=/usr/bin/primer3_core (The full path to the primer3_core executable) PRIMER3_CONFIG=/opt/primer3_config/ (The primer3_config directory that is found in the primer3 distribution, see above) PLAYRDESIGN_DATA=/opt/PLAYRDesign_data (The directory containing the EST and exon data, see above)
PLAYRDesign Output
I have attached a sample of the output probes from the C-probe designer: C Probe Analysis SOD1/VIM (pdf) C Probe Analysis SOD1/VIM (docx)