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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.
| Code Block |
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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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