Daniel:Notebook/HiResChrPaint/2014-6-20: Difference between revisions

From ZhangLabWiki
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)

Back to Calendar

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...

  1. Run OligoArray2
    1. 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 &