Daniel:Notebook/HiResChrPaint/2014-6-16: Difference between revisions
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#Download fasta file from ncbi. | #Download fasta file from ncbi. | ||
*[http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/|NCBI hg38 download] | |||
#Concatenate .fa files; oligopaints, etc. needs a single reference file | |||
## cat *.fa > hg38.fa |
Revision as of 23:01, 16 June 2014
Probe Design
Using the Oligopaints scripts by Beliveau, my goal is to design a positive/negative control for the FISH probes. The control is to focus on a region of the X chromosome, yet to be determined. Using male cells (such as PGP1), exactly one region should be painted per cell. This serves as a potential positive and negative control.
Probe Mining
Scripts:
Setting up the scripts for probe mining. I'm doing this locally on my machine for now, following the instructions in the two pdfs above.
Setting up a BLAST Database
Required for running the Oligopaints scripts.
- Download fasta file from ncbi.
- Concatenate .fa files; oligopaints, etc. needs a single reference file
- cat *.fa > hg38.fa