RNAseq for lncRNA

[wtrypste]

Hi all,

I am a new member of this RNAseq forum and a first year PhD student. I want to look at lncRNA profiling using RNAseq (illumuna hiseq 2000).

Any general advice would be very helpfull but I also have some specific questions:
1) How deep I have to sequence to find them, i.e.how many reads per sample?
2) paired end sequencing: I know what a paired end read it but why is it better? Is it just the coverage that is improved?

thanks in advance
grts

[HSV-1]

The same issues are bothering me here.

What I am gonna do is to ChIP-seq with Pol III antibody to see the occupancy on chromatin that is not protein coding region.