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We have already installed breseq in $BI/bin
, so you should be ready to go! Skip this section.
Download breseq from Google code
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You do not need to install a compiler (GCC/ICC), bowtie2, or R on TACC as they are available via the module system.
You could add these commands to your $HOME/.profile_user if you wanted them available by default. |
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Because this data set is relatively small (roughly 100x coverage of a 48,000 bp genome), a breseq run will take < 5 minutes. Submit this command to the TACC development queue.
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breseq -j 12 -r lambda.gbk lambda_mixed_population.fastq > log.txt
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If you use To figure out the full path to your file, you can use the
Then try a command like this on your desktop (if on a Linux machine or MacOS X):
It would be even better practice to archive and gzip the |
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breseq includes a few utility commands that can be used on any BAM/FASTA set of files to draw an HTML read pileup or a plot of the coverage across a region.
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breseq bam2aln NC_012967:237462-237462
breseq bam2cov NC_012967:2300000-2320000
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You can It's easiest to run these commands from inside the main output directory (e.g., output_20K
) of a breseq run. They use information in the data
directory.
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breseq bam2aln NC_012967:237462-237462
breseq bam2cov NC_012967:2300000-2320000
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Additionally, the files in the data
directory can be loaded in IGV if you copy them back to your desktop.
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