Daniel:Notebook/HiResChrPaint/2014-6-24: Difference between revisions
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==Probe Mining== | ==Probe Mining== | ||
Well, it started [[Daniel:Notebook/HiResChrPaint/2014-6- | 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]
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.
- 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.