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)

Back to Calendar

Probe Mining

From yesterday's results I know that I need to move the files and programs to genome miner to run.

  1. Install oligoarrayaux
    1. ./configure --prefix=$HOME
    2. make
    3. make install
  2. Run OligoArray2 using the blast available on genome miner
    1. 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.

  1. Create blast database
    1. formatdb -i hg38.fas -p F -o T