May I please know what commands I should use to combine two bed files but with no common data set in the resulting bed file?

This seems like a different question. You can use BEDOPS bedops --not-element-of to remove elements from one BED file that overlap those in a second BED file:

$ bedops --not-element-of 1 first.bed second.bed > answer.bed

In this example, the file answer.bed contains elements exclusive to the file first.bed.

I recommend using BEDOPS sort-bed to sort BED files to use with BEDOPS tools. It runs faster than GNU sort and has fewer restrictions than other tools:

$ sort-bed unsorted.bed > sorted.bed

As in the website of Bedtools: http://bedtools.readthedocs.org/en/latest/content/tools/merge.html

bedtools merge requires that you presort your data by chromosome and then by start position (e.g., sort -k1,1 -k2,2nin.bed > in.sorted.bed for BED files).

then you can

bedtools merge [OPTIONS] -i <BED/GFF/VCF/BAM>

after merge all files you want to remove duplicates,

I found a discussion about this here: https://groups.google.com/forum/#!topic/bedtools-discuss/2o7oUgBwebw

As they suggested, you must define duplicates.

[1] "Want you to remove entries where _every_ column is identical?" (easy) or

[2] "Want you to remove entries where the coordinates are the same but for example, the names are different?" (not easy)

I suggest you to look at the link and see the entire discussion but, it seems that you could on the bash shell use this:

sort -k1,1 -k2,2n -k3,3n -u <BED> > output_sorted_uniq.bed # and this can remove duplicates

Thank you Tiago. I have created a bed file with repeats by combining two. Now, I have to remove the repeats/duplicates. I will go through the link you provided and will see how far I can figure it out. Thank you