RPKM and read counts from RNA-seq

[rakesh12]

Hi All,
I have alignment files from RNA-seq data in .sam format. I want to calculate read counts and RPKM values using RefSeq reference data (refseq.gft) file for several samples. I tried to use HTSeq, TopHat etc but I have not be able to get RPKM and read counts. Can you please suggest appropriate bioinformatics tools?
Thanks for your help,
Rakesh

[pbluescript]

Tophat is meant to align reads, not give you expression values.
Try Cufflinks or rsem.
HTSeq will give you the count data which you could convert into a normalized value if you wish.