[DrJay]

Thanks for all your help GenoMax

Good times - Ive doubled my knowledge of Linux in the past 24 hours trying to work this out

Bad times - It helps if you are running Linux on a Mac VM to download the program for Linux, not for the Mac

Oh well. . . .
Working now ;-)

[GenoMax]

You could have done all this on the Mac in the fist place!

BTW: If you are going to continue working with NGS data it would definitely help to go over this guide: http://korflab.ucdavis.edu/Unix_and_...ent.html#part1

[DrJay]

Yep it would have been easier. Its just an intro course I did a while back was all done on Linux so felt more comfortable to start on that but I take your point!

Thanks for the reference though. lots to learn!