How can I compute gene expression for a set of RNA reads? I'm trying to compute a gene expression profile for an organism. I have gene nucleotide sequences of the mentioned organism stored in a fasta file and a set of paired reads stored in two separate files with the same fasta format. Now I want to compute the coverage of every gene by the given reads. That is, on average how many reads cover a given segment of the sequence.

Is there any tool for this specific purpose?
I'm trying to use the velvet sequencer but I have encountered a few problems.
It's unclear if your paired-end reads are actually in fasta format, I'll presume that they're in fastq instead.

The easiest tool to use is salmon, which nicely deals with things like multimapping. If you're trying to judge the quality of an assembly, then I recommend having a look at transrate, which uses some related methodology for assessing contig quality.