Daniel:Notebook/HiResChrPaint/2014-6-16

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Revision as of 00:31, 17 June 2014 by >Djacobse (→‎Probe Mining)
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Probe Design

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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.

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