Daniel:Notebook/HiResChrPaint/2014-6-17

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Probe Design (Started 06/17/2014)[edit]

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Probe Mining[edit]

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
  2. Run OligoArray2 using new blast database
    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

This command runs for a long time. This command didn't work either. The memory allocation by java was too small. As such, I will run the command again using larger memory allocation.