Daniel:Notebook/HiResChrPaint/2014-6-16
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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.
- Download fasta file from ncbi.
- Concatenate .fa files; oligopaints, etc. needs a single reference file
- cat *.fa > hg38.fa
- Download gene information for a specific region
- Selected CASK gene, Xp11.4 (chrX:41514933-41923154); arbitrary
- Generate BLAST database using makeblastdb
- make a directory called BlastDb
- set up a link using ln -s to the .fas file
- makeblastdb -in hg38.fas -out hg38 -dbtype nucl -parse_seqids
- Run OligoArray to