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]
[http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/|NCBI hg38 download]
#Concatenate .fa files; oligopaints, etc. needs a single reference file
#Concatenate .fa files; oligopaints, etc. needs a single reference file
## cat *.fa > hg38.fa
## cat *.fa > hg38.fa

Revision as of 23:02, 16 June 2014

Probe Design

Back to Calendar

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.

  1. Download fasta file from ncbi.
hg38 download
  1. Concatenate .fa files; oligopaints, etc. needs a single reference file
    1. cat *.fa > hg38.fa