We are about to do our first RNA-seq (ABI Solid, mouse mRNA) experiment with our local genome core. They're new to this as well. I have to answer the question, "how many reads do you want per sample?". The core has an estimate of the percent of reads likely to map from ABI, and has derived an estimate of how many mapped reads to expect per lane. The samples are normal epithelium, triplicates or quadruplicates of three distinct strains of mouse, so 9 or 12 individual samples. We will be comparing results to existing microarray results from the same animals.
Are there any well-founded rules of thumb to answer this question? Any advice, either informal or published?