Add all non overlapping genes/transcripts from one gtf to another with bedtools intersect

Question

[robert.murphy]

If trying to add all non-overlapping transcripts from one gtf to another gtf would would the appropriate bedtools intersect command be.

I am starting with:

intersectBed –wa –a augustus.gtf –b genemark.gtf > mynew.gtf

But I think this will only write the original entry in A for each overlap but not the non overlapping parts?

[ATpoint]

Option -v is what you want.

[robert.murphy]

So use -v to get non overlapping then later on join the two together?

[ATpoint]

That could be an option, yes.

[robert.murphy]

Is there a better way you would suggest?