Daniel:Notebook/HiResChrPaint/2014-6-16

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Revision as of 23:14, 16 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.

Setting up a BLAST Database

Required for running the Oligopaints scripts.

  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