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This was extensively covered in the Advanced Breseq tutorial. You may want to review this section of the tutorial for more detailed explanation while you wait for the 2 runs to complete. Check which commands are still running using the jobs command and the tail command listed above.
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.
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Once you have transferred the trimmed_vs_SSCS.html file back to your computer, open it and scroll around to see what the effects of our SSCS error correction were.