In recipes that call for Jalapeno peppers you can substitute the red pepper flakes for Jalapeno Peppers.
Red Pepper Flakes are made from crushed Cayenne peppers so it can be substituted for Jalapeno peppers.
If you don't have Jalapeno peppers or fresh serrano chilies, the best substitutes are fresh habaneros, gueros or jalapenos.
But If you don't have these, however, you can use readily available crushed red pepper flakes, which are typically made from dried cayenne peppers.
I've used red pepper flakes in place of Jalapeno before and it turned out just fine for the recipe.
You can also crush up dried Jalapenos and make red pepper flakes or make crushed peppers from fresh dried Jalapeno peppers to add to your recipes or Chili etc.