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gdtools compare -h |
the above will display instructions stating that gdtools compare needs a genebank (gbk) reference file, and .gd files to compare. The -o command is used to direct the output to a specific file name and/or location. | Expand |
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gdtools compare -o stat_comparison.html -r reference/REL606.6.gbk breseq_output/with_stats/output/output.gd breseq_output/without_stats/output/output.gd |
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All of the necessary files to complete our analysis have now been generated, but not in the most usable forms. In order to facilitate an easier transfer of the breseq output two small helper scripts have been placed in the $BI/gva_course/mixed_population/helper_scripts folder (export-breseq and batch-run.pl). Copy both files into the breseq_output directory and then run the export-breseq script by just typing its name from within the breseq_output directory.
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cp $BI/gva_course/mixed_population/helper_scripts/export-breseq breseq_output
cp $BI/gva_course/mixed_population/helper_scripts/batch_run.pl breseq_output
cd breseq_output
export-breseq |
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You should now have 2 files that now need to be to your local computer to visualize the data: 05_Output_Export.tar.gz and stat_comparison.html. Alternatively, these files can be downloaded from the barricklab server at: