Daniel:Notebook/ComboLock/CProbeDesign: Difference between revisions
Jump to navigation
Jump to search
>Djacobse |
>Djacobse |
||
Line 12: | Line 12: | ||
*[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 start="2">Make blast databases | |||
<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> | |||
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
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: