ls function in windows bash terminal not showing all files

Question

[truebeliever24]

I am pretty new to bioinformatics, and just installed bash and ubuntu on my PC. When I use the 'ls' command for my home directory, it shows only a few of the files and folders. It also neglects to show my genome vcf file. Terminal also does not recognize that there is a vcf file present when i try to read it in using vcftools....I'm thinking these problems are related. I've had success on the Mac computers in my lab on campus. Please help!

Thanks.

[jflopezfernandez]

Try using ls -a to show hidden files as well.

[GenoMax]

Simple explanation is the files are not where you think they are. Are you trying to access files that are present in directories present in windows side of things?

Answer 1

[truebeliever24]

I figured it out, thanks everybody! Some of my files didn't have permission. So I used the ls -a to find out which files those were, then used sudo chmod 777 filename to enable access to them via terminal.

[jflopezfernandez]

Hey, glad to hear you figured it out. If I can offer a pointer or two, by convention you probably want your folders at 755 and files at 644. A 755 means that everyone can read and write to the directories, but only you have write access. A 644 for your files means that everyone has read access, but no write or execution privilege, and you have read and write privileges, but will have to explicitly make the file executable should you wish to do so.

This is more in tune with the balance between sanity and security, as opposed to the 777 situation, where your computer becomes a literal free for all for anyone who gets access.