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Code Block
languagebash
titlesuggested direcotry directory set up
cds
cp -r $BI/gva_course/structural_variation/data sv_tutorial
cd sv_tutorial

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Warning
titleDo not run on head node

Many of the commands past this point are computationally intensive. You should run them through an idev shell or by qsub. We recommend idev for the tutorial, but you could also qsub any command that takes more than a few seconds to complete.

Code Block
titleExample command to start an idev shell
idev -m 60 -q development -A CCBB"UT-2015-05-18"
Code Block
bowtie2-build NC_012967.1.fasta NC_012967.1
bowtie2 -p 12 -X 5000 --rf -x NC_012967.1 -1 61FTVAAXX_2_1.fastq -2 61FTVAAXX_2_2.fastq -S 61FTVAAXX.sam

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