Like the previous exercise, we can use RSEM to estimate the expression levels of the re-constructed transcripts under the four conditions: logarithmic growth, plateau phase, heat shock and diauxic shift. First, we align the RNA-Seq reads to the Trinity transcripts using Bowtie. Then we run RSEM to estimate the number of reads mapped to each transcript. We do not need a splice-aware aligner (such as STAR) in this case because we are mapping the reads to cDNAs instead of a genomic sequence. Also the gap-free alignment produced by Bowtie is used as input for RSEM.