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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.
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cds cp -r $BI/gva_course/structural_variation/data BDIB_sv_tutorial cd BDIB_sv_tutorial |
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Make sure you are on an idev node using the command: showq -u
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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.
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1<tab>NC_012967<tab>4629812 # Use the tab key rather than writing out <tab>!! |
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Optional: Install SVDetectWe 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 Install SVDetect scriptsNavigate to the SVDetect project page More information: Download the code onto TACC.
Move the Perl scripts and make them executable
Install required Perl modulesSVdetect 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:
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