Daniel:Notebook/HiResChrPaint/2014-6-20: Difference between revisions
Jump to navigation
Jump to search
>Djacobse |
>Djacobse |
||
Line 10: | Line 10: | ||
#Run OligoArray2 | #Run OligoArray2 | ||
##java -jar /home/djacobse/blastdb_hg38/OligoArray2_1/OligoArray2.jar -i in_caskgene.fas -d hg19.fas -o oligo_caskgene.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 & | ##java -Xmx4096m -jar /home/djacobse/blastdb_hg38/OligoArray2_1/OligoArray2.jar -i in_caskgene.fas -d hg19.fas -o oligo_caskgene.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 & |
Revision as of 20:35, 20 June 2014
Probe Design (Started 06/17/2014)
Probe Mining
Well, it took a while, but the OligoArray script finished running and...
The Oligo.txt file has nothing in it. Most probes were denied due too high of a Tm. Guess I've got to redo the script but with bigger range for Tms. Sigh...
- Run OligoArray2
- java -Xmx4096m -jar /home/djacobse/blastdb_hg38/OligoArray2_1/OligoArray2.jar -i in_caskgene.fas -d hg19.fas -o oligo_caskgene.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 &