How do I find read depth?

[cnyh]

With Illumina RNA-Seq data that I've analyzed via TopHat/Bowtie and cufflinks/cuffdiff, what command can I use to find out what the read depth of my samples is?

[jgibbons1]

You can use samtools depth or samtools mpileup to retrieve coverage values from your mapping output (sorted bam file). You can then sum the depth per site and divide that number by the number of sites in the reference transcriptome.