How do I run this perl script proprerly to get GC percent from multiple fasta files?

Question

[natt1621]

Hi. I just found this script on Researchgate (https://www.researchgate.net/post/How-can-I-estimate-the-GC-content-of-a-genome) to get the GC content from fasta files (all the rights of this script go to Jennifer Meneghin, July 23, 2009), but I don't know clearly how to run it. I use Windows 10 x64 and I downloaded the Pearl interpreter (strawberry-perl-5.32.1.1-64bit). I run it through cmd on windows, executing the .pl file but I don't know how to input the secuences. I'm kind of new in this bioinformatics and scripts world, so any help would be appreciated. This the header of the script.

http://ibb.co/kcffTBx

[rpolicastro]

If your using windows, it's better to use the windows subsystem for linux (WSL) in general so that you can run linux (almost natively) on windows.

I would also recommend seqtk comp or seqkit fx2tab as alternatives.

[natt1621]

Thank you so much, I will take a look to it.

Answer 1

[Joe]

The script tells you its usage:

perl scriptname.pl <fasta file>

You simply need to write the filepath/name of the fasta file in afterwards. You need a space after the scriptname, but do not include the < or > as these are just used to denote 'placeholder' values.

[natt1621]

Thank you so much. I can write the name of the fasta file or its path so the script can recognize the file, right?

[Joe]

Yes, but if your working directory isn't the directory where the file is, you will need to provide the absolute or relative filepath, rather than just the filename.