S1 Table

There are several downstream analysis goals for which RNA-seq is well suited. Main categories of these are described briefly below with reference to supporting materials. Refer to S2 Table for specific tools relevant to many of these areas. For each application, a basic data recommendation is provided. It is important to remember that these are simply examples. In addition to the varying demands of each analysis technique, data requirements will depend heavily on the size and complexity of the genome, the complexity of the transcriptome, the method of RNA isolation and library preparation, the need to robustly detect transcripts with low copy numbers, and many other factors. For the purposes of this table, low RNA-seq depth is 5-25M reads, moderate depth is 25-100M reads, and high depth is 100-500M. Similarly, short reads are 50-200bp and long reads are 200-500bp.