How do you make part of the Standard Shader transparent?

I have a diffuse texture and an alpha map with the opaque parts colored white and the transparent parts colored grey.

The standard shader only has a slot for the albedo map so I cannot work out where to put the alpha texture so only the glass of my modular window asset is transparent. Any suggestions?

@mattockman:

Hi, check out this link:

If the the Standard shader is set to transparent or cutout the transparency values will be used from the alpha channel of the Albedo texture / color.

If you hover with your mouse over the different texture slots, unity will show you what channels are used from that texture.
More information about transparency in the standard shader you can get on this documentation page:

My problem was pretty basic. I simply didn’t know how to create alpha channels and how to save them appropriately (I was saving to PNG as opposed to Targa). I’ve since learned how to do this in photoshop thanks to this tutorial: Unity3D Tutorial #5 [ Alpha Textures ] - YouTube