Daniel:Notebook/HiResChrPaint/2014-6-17: Difference between revisions
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>Djacobse (Created page with "=Probe Design (Started 06/17/2014)= Back to Calendar ==Probe Mining== From [[Daniel:Notebook/H...") |
>Djacobse |
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##make | ##make | ||
##make install | ##make install | ||
# | #Run OligoArray2 using the blast available on genome miner | ||
##java -jar /home/djacobse/blastdb_hg38/OligoArray2_1/OligoArray2.jar -i in_caskgene.fas -d hg38.fas -o oligo_caskgene.txt -r rejected_oligo.fas -R caskgene.log -n 30 -l 60 -L 60 -D 1000 -t 55 -T 65 -s 70 -x 70 -p 35 -P 80 -m "CCCC;GGGG;TTTTT;AAAAA" -g 2 | |||
Can OligoArray read/write specified files? NO | |||
Data initialization: DONE | |||
Is hg38.fas a valid Blast database? NO | |||
Is OligoArrayAux installed? YES | |||
So something is still up. I'm going to try rewriting the Blast database using formatdb, which is available on this version of blast. | |||
#Create blast database | |||
##formatdb -i hg38.fas -p F -o T |
Revision as of 22:10, 17 June 2014
Probe Design (Started 06/17/2014)
Probe Mining
From yesterday's results I know that I need to move the files and programs to genome miner to run.
- Install oligoarrayaux
- ./configure --prefix=$HOME
- make
- make install
- Run OligoArray2 using the blast available on genome miner
- java -jar /home/djacobse/blastdb_hg38/OligoArray2_1/OligoArray2.jar -i in_caskgene.fas -d hg38.fas -o oligo_caskgene.txt -r rejected_oligo.fas -R caskgene.log -n 30 -l 60 -L 60 -D 1000 -t 55 -T 65 -s 70 -x 70 -p 35 -P 80 -m "CCCC;GGGG;TTTTT;AAAAA" -g 2
Can OligoArray read/write specified files? NO Data initialization: DONE Is hg38.fas a valid Blast database? NO Is OligoArrayAux installed? YES
So something is still up. I'm going to try rewriting the Blast database using formatdb, which is available on this version of blast.
- Create blast database
- formatdb -i hg38.fas -p F -o T