Find Differentially Expressed Genes given BAM files

[mrzombie]

I was recently given two sets of BAM files, and would like to compare them to find the differentially expressed genes. When I tried cufflinks, however, I eventually found that I did not have an accepted_hits.bam file, which would have been generated by the fastq files. After briefly entertaining notions of converting BAM to fastq back to BAM, I realized that was just silly.

What is the most straightforward way to proceed from here?

[mastal]

Find Differentially Expressed Genes given BAM files

Run tophat, then run cufflinks.