Detecting duplicates in multiple files and printing the unique results to a file

I am trying to compare two (or more) files, containing chromosomal positions in the form 2:282828282828, there are about 70,000 of these positions, and whilst Excel works for smaller datasets, it is causing me too much trouble on this scale.

What I was trying to do is 1) compare each position in the matrix with every position in the other matrix, and if the value is unique, print that value to a new file OR 2) compare all cells in a merged file, and print the unique values in to a different file.

I am a little stuck as to where to start for the first option.

But for the second option, I was thinking of this:

dataset1=a [n, bin] = histc(a, unique(a)); multiple = find(n > 1);

to find the multiple values, but how do I get MATLAB to write the unique values where n=1 to a new file?