Help! How to calculate gene expression level (RPKM) in RNA-seq experiment

[fgh1124]

HI, everyone!

I just want to know each gene's expression level not the transcript isoforms. I have alignment data formated in SAM/BAM and annotation file in gtf/gff/bed. Some genes position have overlap with other genes. So I want to know which software is suitable for my question except for cuffdiff or cufflinks?

Thanks for your time!

[pbluescript]

You could try RSEM:

http://deweylab.biostat.wisc.edu/rsem/

[Mike2188]

Both cufflinks and cuffdiff will generate FPKM data. Cuffdiff will also spit out differentially expressed genes between your samples and take a bit longer.