Analyzing differential expression of de novo assembled transcriptomes using RSEM

We already discussed assembly of single transcriptome in our Tutorial for RNA-Seq de novo assembly using Trinity. To compare transcriptomes of several samples, it is recommended to start analysis in slightly different way. At first you need to assemble transcriptome using reads of all your samples. Then you align reads of each sample to this common transcriptome separately and compare the results. We will start this tutorial with transcriptome assembled from reads of two samples obtained from two ganglion of medical lynch.