Page Comparison

...

cp -r /corral-repl/utexas/BioITeam/ngs_course $WORK/GVA2016  &  # this will run the command in the background and hopefully not cause problems
# because the absolute path to both where the folder is, and where you want it to be are provided, this command can be executed anywhere. 
# Absolute paths differ from relative paths in that they start with a / rather than a . or the name of a folder/file (which is assumed to have started with a .)
# This will likely take a few minutes, and produce messages such as:
# cp: cannot open `/corral-repl/utexas/BioITeam/ngs_course/IGV/.DS_Store' for reading: Permission denied

...

 
mkdir $WORK/tutorial_1
cp /corral-repl/utexas/BioITeam/ngs_course/lambda_mixed_pop/data/lambda_mixed_population.fastq $WORK/tutorial_1
cp /corral-repl/utexas/BioITeam/ngs_course/lambda_mixed_pop/data/lambda.gbk $WORK/tutorial_1
 
mkdir $WORK/tutorial_2
cp /corral-repl/utexas/BioITeam/ngs_course/ecoli_clones/data/* $WORK/tutorial_2

Now that we have all of the data that we want in our work directory, lets move the lambda phage data to scratch so we can begin using it. The following 2 files are in the lambda_mixed_pop/data directory inside of your newly created GVA2016 directory:

...

mkdir $SCRATCH/BDIB_breseq_tutorial_1_1
 
# Try the following commands, if they do not work, skip them and try the next 2 commands
cp $WORK/GVA2016/lambda_mixed_pop/data/lambda_mixed_population.fastq $SCRATCH/BDIB_breseq_tutorial_1
cp $WORK/GVA2016/lambda_mixed_pop/data/lambda.gbk.gbk $SCRATCH/BDIB_breseq_tutorial_1
 
# IF the above 2 commands worked, do not try these commands. If the previous 2 failed, use this instead.
cp $WORK/tutorial_1/* $SCRATCH/BDIB_breseq_tutorial_1

...

A bunch of progress messages will stream by during the breseq run which would clutter the screen if not for the redirection to the log.txt file. The & at the end of the line tells the system to run the previous command in the background which will enable you to still type and execute other commands while breseq runs. The output text details several steps in a pipeline that combines the steps of mapping (using SSAHA2), variant calling, annotating mutations, etc. You can examine them by peeking in the log.txt file as your job runs using tail -f log.txt. The -f option means to "follow" the file and keep giving you output from it as it gets bigger. To stop the tailing command hit ctrl-c which is the keyboard interrupt signal. While breseq is running lets look at what the different parts of the command are actually doing:

...

Now we'll try running breseq on some Escherichia coli genomes from an evolution experiment. These files are larger. 

Data

The data files for this example are in the following path. Go ahead and copy them to a new folder in your $SCRATCH directory called . 

Data

The data files for this example are in the following path. Go ahead and copy them to a new folder in your $SCRATCH directory called BDIB_breseq_tutorial_2:

$WORK/GVA2016/ecoli_clones/data

mkdir $SCRATCH/BDIB_breseq_tutorial_2

...

 
# Try this command first, if it does not work use the alternative command
cp $WORK/GVA2016/ecoli_clones/data

mkdir/* $SCRATCH/BDIB_breseq_tutorial_2
 
# Use this command if the previous copy command does not work:
cp $WORK/GVA2016/ecoli_clones/datatutorial_2/* $SCRATCH/BDIB_breseq_tutorial_2
cd $SCRATCH/BDIB_breseq_tutorial_2

...