You can do this by adding this code into the Script Editor -> Remotes tab into a new file (File -> New) from menubar.

Place the channel name and when you hit the "F2" f-key from the keyboard it will mark it as read, also you can change the 'f2' to what ever f-key you want, or you can use it manually like: /markasread #CHANNEL

Code:

Code:
alias f2 { markasread #CHANNEL-NAME-HERE }
alias markasread {
  if (!$1) { echo 4 -a Error: Please specify a channel! | return }
  if (!$window($1)) { echo 4 -a Error: The $qt($1) channel window does not exists! | return }
  window -g0 $qt($1)
}