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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 -aA CCBB
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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Very, Very Advanced Exercise

  • SVDetect has a nice option to output a file that can be read by Circos to produce drawings.

    Expand
    titleHere's a completely untested hint of an addition to your .conf file for circos
    Code Block
    titleThis is untested...
    <circos>
organism_id=fish
  <colorcode>
    255,0,0=1,4
    0,255,0=5,10
    0,0,255=11,100000
  </colorcode>
</circos>