Daniel:Notebook/HiResChrPaint/2014-6-24
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Probe Design (Started 06/17/2014)
Probe Mining
Well, it started Friday, but at some point over the weekend my probe mining finished. There are 2 GB of 60 bp oligos, amounting to approximately 40k potential sequences. Now I should be able to run Oligopaints scripts on them in order to generate probe files of the desired sequences/properties.
- Clean oligo.txt file to make it into a bed file
- python ../../Probe_Design/bin/clean_file.py
Now I can run whatever Oligopaints scripts I want on it. However, caskgene was always supposed to be a placeholder, so I took a good look into genes on the X chromosome. I think dystrophin will do nicely. It is the gene associated with Duchenne's Muscular Dystrophy, and is found on the X chromosome.
Dystrophin chrX: 31119228-33211556 (hg38); chrX:31137345-33229673 (hg37);
So armed with that knowledge (and using hg19 since that is the build from the Wu lab), I'll tackle dystrophin.
- Separate fasta file into 1kb blocks
- python ../bin/input_blocks.p
- Please enter the filename, "chr2R_sorted_oligo.txt" or "chr2R_intersect.bed" etc.: dystrophin.fa
- Please enter the chromosome or assembly, "chr1 or ch2R, etc.: chrX
- Create blast database
- formatdb -i hg19.fas -p F -o T