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Here's an E. coli genome re-sequencing sample where a key mutation producing a new structural variant was responsible for a new phenotype involving citrate, one of Dacia's favorite topics.

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

...

Warning
titleDo not run on head node

Make sure you are on an idev node using the command: showq -u

Code Block
titleIf you need a new idev node
collapsetrue
idev  -m 60120 -r CCBB_Bio_Summer_School_2016_Day25.23.17PM -A UT-2015-05-18 -N 2 -n 8
Code Block
bowtie2-build NC_012967.1.fasta NC_012967.1
bowtie2 -p 48 -X 5000 --rf -x NC_012967.1 -1 61FTVAAXX_2_1.fastq -2 61FTVAAXX_2_2.fastq -S 61FTVAAXX.sam

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You also need to create a tab-delimited file of chromosome lengths named NC_012967.1.lengths. YOU CAN NOT COPY PASTE THIS COMMAND! Use the nano command.

Code Block
titleFile NC_012967.1.lengths
1<tab>NC_012967<tab>4629812  # Use the tab key rather than writing out <tab>!!

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Expand
titleclick here for installation instructions

Optional: Install SVDetect

We have installed SVdetect for you already as installation is a bit difficult (though still much easier than the alternatives listed in the introduction). You can verify it's location using which SVDetect in your $PATH under $BI/bin. One of the advantages (or disadvantages) of using the communal resource is that someone else can update all the necessary programs and packages for you. Alternatively, you can make a personal copy of the program yourself using the following commands. NOTE that this is presented mostly to underscore how spoiled we are with modules and the BioITeam.

Install SVDetect scripts

Navigate to the SVDetect project page

More information:

Download the code onto TACC.

Code Block
wget https://sourceforge.net/projects/svdetect/files/latest/download
tar -xvzf SVDetect_r*.tar.gz
cd SVDetect_r*

Move the Perl scripts and make them executable

Code Block
cp bin/SVDetect $HOME/local/bin
chmod 775 scripts/BAM_preprocessingPairs.pl
cp scripts/BAM_preprocessingPairs.pl $HOME/local/bin

Install required Perl modules

SVdetect requires a few Perl modules to be installed. In the default TACC environment, you can use the cpan shell to install most well-behaved Perl modules (with the exception of some complicated ones that require other libraries to be installed or things to compile). Here's how:

Code Block
titleInstall Perl modules required for SVDetect
login1$ module load perl
login1$ cpan
...
cpan[4]> install Config::General
...
cpan[4]> install Tie::IxHash
...
cpan[4]> install Parallel::ForkManager
...
cpan[4]> quit
login1$