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Daniel:Notebook/HiResChrPaint/2014-6-24
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=Probe Design ([[Daniel:Notebook/HiResChrPaint/2014-6-16|Started 06/17/2014]])= [[Daniel:Notebook/HiResChrPaint|Back to Calendar]] ==Probe Mining== Well, it started [[Daniel:Notebook/HiResChrPaint/2014-6-20|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 ##LOGFILE OUTPUT: Formatted 3095689 sequences in volume 0 ##SUCCESS: formatted database hg19.fas #Run OligoArray2 for dystrophin ##java -Xmx4096m -jar /home/djacobse/blastdb_hg38/OligoArray2_1/OligoArray2.jar -i in_dystrophin.fas -d hg19.fas -o dystrophin_oligo.txt -r rejected_oligo.fas -R caskgene.log -n 30 -l 60 -L 60 -D 1000 -t 35 -T 95 -s 70 -x 70 -p 35 -P 80 -m "CCCC;GGGG;TTTTT;AAAAA" -g 2 Now I am consistently getting this error: Is OligoArrayAux installed? NO However, OligoArrayAux is most definitely installed. I tried reinstalling oligoarrayaux a couple of times, and eventually the command above started working, so... we'll see I guess. [[Category:HRCP]] [[Category:Probe Mining]] [[Category:OligoArray]]
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