Reference transcriptome - how to select

[adrian]

Hi:

I have RNA-seq data set (single end ; 36mer).

I want to choose RefSeq or equivalent from other sources (ENSEMBL or UCSC).

If I am chose RefSeq (NCBI), the header information is not exactly compatible with UCSC annotations.

What is the general practice . I am analyzing RNA-Seq for the first time, I worked on Exome-Seq prior to this.

thanks
Adrian