Daniel:Notebook/HiResChrPaint/2014-6-24: Difference between revisions

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>Djacobse
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==Probe Mining==
==Probe Mining==


Well, it started [[Daniel:Notebook/HiResChrPaint/2014-6-21|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.
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]]

Latest revision as of 18:00, 2 July 2014

Probe Design (Started 06/17/2014)[edit]

Back to Calendar

Probe Mining[edit]

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.

  1. Clean oligo.txt file to make it into a bed file
    1. 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.

  1. Separate fasta file into 1kb blocks
    1. python ../bin/input_blocks.p
    2. Please enter the filename, "chr2R_sorted_oligo.txt" or "chr2R_intersect.bed" etc.: dystrophin.fa
    3. Please enter the chromosome or assembly, "chr1 or ch2R, etc.: chrX
  2. Create blast database
    1. formatdb -i hg19.fas -p F -o T
    2. LOGFILE OUTPUT: Formatted 3095689 sequences in volume 0
    3. SUCCESS: formatted database hg19.fas
  3. Run OligoArray2 for dystrophin
    1. 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.