RNA-seq data analysis

[quix]

Hi_all:

Just got the final result of my RNA-seq data quantitation analysis.

I have some questions now:

1. Usually which RPKM value do you use for cut-off?
When the gene expression(in RPKM) is bigger than 0.1, its expression will be counted?

2. In the final result, I get the list of genes in UCSC gene format, like uc007akt.1. However, sometimes several entries has a same gene name, in this case shall I add the RPKM value together from these entries and take the sum as the expression level of the gene?

Thanks very much

[bioinfosm]

Dont have much detail to add but adding does not really sound right.. also, I believe most people do differential expression and thus use ratio of rpkm.