Working with Files

Creates a new directory called rnaseq_analysis in your current location. Nothing is printed if successful.

The new directory appears in the listing. The 'd' at the start indicates it's a directory.

Creates three directories with a single command. Separate multiple names with spaces.

All three directories were created.

This fails because the parent directory 'qc_reports' doesn't exist yet. mkdir doesn't create intermediate directories by default.

The -p flag creates all necessary parent directories. Now results, qc_reports, and fastqc are all created in one command.

Creates a project with six subdirectories in one command. The curly braces {} are expanded by the shell to create multiple directories.

All six directories were created from a single command.

Creates a copy of sample.fastq.gz named backup_sample.fastq.gz in the same directory. Original file remains unchanged.

Copies sample.fastq.gz into the raw_data directory. The file keeps the same name in the destination.

Copies and renames in one command. The file is copied to raw_data with a new name.

Copies multiple files to the same destination. The last argument must be a directory.

Copy all FASTQ files at once using a wildcard. The * matches any characters, so this copies every file ending in .fastq.gz.

Copying directories requires the -r (recursive) flag. Without it, cp refuses to copy directories.

The -r flag copies the directory and all its contents recursively. Now backup_scripts contains everything from scripts.

The -p flag preserves timestamps, permissions, and ownership. Useful when you need to maintain file metadata.

Renames old_name.fastq.gz to new_name.fastq.gz in the same directory. The original name no longer exists.

Moves sample.fastq.gz into the raw_data directory. The file no longer exists in the original location.

Moves the file from results to archive while also renaming it. Combines moving and renaming in one command.

Move all BAM files to the alignments directory. The * wildcard matches all files ending in .bam.

The -i flag prompts before overwriting. If important_file.txt already exists in results/, you'll be asked to confirm.

Renames all .txt files to .processed.txt. For example, data.txt becomes data.processed.txt. The loop processes each file individually.

Deletes temporary_file.txt permanently. No confirmation, no recovery. The file is gone.

The -i flag prompts for confirmation before deleting. Type 'y' for yes or 'n' for no.

Deletes multiple files. All three are removed permanently.

Deletes all files ending in .tmp. Be very careful with wildcards - verify files first with ls *.tmp before deleting.

Regular rm cannot delete directories. This is a safety feature to prevent accidentally removing entire directory trees.

The -r flag recursively deletes the directory and everything inside it. This cannot be undone.

The -f flag forces deletion without prompting. Extremely dangerous. The -rf combination is the most destructive command in UNIX.

Create a trash directory in your home folder (one-time setup).

Move files to trash instead of deleting. You can recover them if needed.

Empty the trash when you're certain you don't need those files. Review contents first with ls ~/.trash/

If results.txt already exists, it will be overwritten without warning. The original results.txt is lost forever.

Check if the file exists before copying. The && means 'run second command only if first succeeds.'

DANGER: Deletes everything in the current directory. Always be explicit about what you're deleting.

Delete only temporary files with .tmp extension. Be specific with your patterns.

The space between * and .tmp makes these two separate arguments. First it tries to delete a file literally named '*', then one named '.tmp'. Neither exists, but if * existed as a filename, it would be deleted.

No space - this is one pattern that matches files ending in .tmp.