non-overlapping features GFF (BEDTools?)

[seqeve]

I have two gff files, one containing transcript sequences, another containing TranscriptionStartSites (TSS).

Now I would like to compare these two gff's and for each transcript sequence find the closest upstream TSS.

Is there a Tool that can do this?
I tried closestbed, but every time a TSS is present inside my transcript sequence it will report this one in stead of looking further. Is there maybe a way to disable reports of overlapping features?

I also looked into the galaxy-flanking_features, from the description this seems to do what I want but it is no longer available on our systems...

Anyone have any tips? Before I start writing my own script...

[dariober]

I tried closestbed, but every time a TSS is present inside my transcript sequence it will report this one in stead of looking further. Is there maybe a way to disable reports of overlapping features?

Hi,
Have you looked at the -io option of closestBed?

-io	Ignore features in B that overlap A.  That is, we want close,
		yet not touching features only

It seems to do what you want...
(I'm not sure if this option has been added in one of the latest features of bedtools.)

All the best
Dario

[seqeve]

Ok, thanks a lot, I guess this will do the job.
Wasn't mentioned at

http://bedtools.readthedocs.org/en/latest/content/closestBed.html

quote: "it does not restrict to closest non-overlapping feature"

But I should of checked the --help before posting here