Use find command but exclude files in two directories

Here’s how you can specify that with find:

find . -type f -name "*_peaks.bed" ! -path "./tmp/*" ! -path "./scripts/*"

Explanation:

• find . – Start find from current working directory (recursively by default)
• -type f – Specify to find that you only want files in the results
• -name "*_peaks.bed" – Look for files with the name ending in _peaks.bed
• ! -path "./tmp/*" – Exclude all results whose path starts with ./tmp/
• ! -path "./scripts/*" – Also exclude all results whose path starts with ./scripts/

Testing the Solution:

$ mkdir a b c d e
$ touch a/1 b/2 c/3 d/4 e/5 e/a e/b
$ find . -type f ! -path "./a/*" ! -path "./b/*"

./d/4
./c/3
./e/a
./e/b
./e/5

You were pretty close, the -name option only considers the basename, where as -path considers the entire path =)