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cp /corral-repl/utexas/BioITeam/gva_course/GVA2022GVA.launcher.slurm breseq.slurm nano breseq.slurm |
| Line number | As is | To be |
|---|---|---|
| 16 | #SBATCH -J jobName | #SBATCH -J SSCSbreseq |
| 17 | #SBATCH -n 1 | #SBATCH -n 2 |
| 21 | #SBATCH -t 12:00:00 | #SBATCH -t 6:00:00 |
| 22 | ##SBATCH --mail-user=ADD | #SBATCH --mail-user=<YourEmailAddress> |
| 23 | ##SBATCH --mail-type=all | #SBATCH --mail-type=all |
| 29 | export LAUNCHER_JOB_FILE=commands | export LAUNCHER_JOB_FILE=breseq_commands |
The changes to lines 22 and 23 are optional but will give you an idea of what types of email you could expect from TACC if you choose to use these options. Just be sure to pay attention to these 2 lines starting with a single # symbol after editing them.
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One the job is complete, Just like the previous tutorial we now want to create a comparison file using "gdtools compare" so we can see the difference of having the trimmed reads vs the SSCS reads. This time you want to create a file "trimmed_vs_SSCS.html".
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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.