Running perl scripts
For the most part, perl script files need to be in the folder where you want them to run. That is, if you want to find out what gRNAs are in the punch sequence, you need the perl script and the sequence to be in the same folder. I recommend having the perl script in a folder, and cycling data in and out of there as needed.
Once you open Terminal and navigate to the folder, you call a perl script with
perl <script name> <other options>
Generally, for my scripts, if you call it without the correct options, it will print out to the Terminal the options it expects.
For example if you type
it will print to the Terminal
Usage: perl multifile.miseq_gRNA_sort.txt <text file with all file names to map, 1 name per line> <24k_grnas_unix.txt>
Usually, opening the file and looking at the comments up top will tell you what the script does, and what it needs to run.
Some scripts require minor tweaks to them. For instance, zv10_repeat_masking.txt changes between folders to grab various files. The script itself needs to be modified so it knows where the repeat files are and where the files to be masked are (as well as the prefix you used when splitting the files). Remember,
will Print the Working Directory give you the file path that that particular script needs.