FPKM of Intergenic Regions

Question

[dennis.s.zhao]

Hello,

I have read that people have used the expression of intergenic regions in order to threshold expression values. I would like to know if there is a way to get the expression values for the intergenic regions. I have seen some links such as the ones below:

http://biopython.org/wiki/Intergenic_regions

http://code.google.com/p/bedtools/wiki/Usage#subtractBed

However, I'm not sure where to go from here.

Any help would be appreciated!

Thanks!

[Michael]

I had a similar problem, did you see my previous post?

You need gene models to calculate average expression, so shuffling the GFF might help.