RSEM is a relatively new bioinformatics tool that has been developed in conjunction with Trinity for the analysis of RNAseq data. RSEM can be used to estimate expression levels for both genes and different isoforms of genes, and is quite quick and easy to use, with an excellent google group for help (“RSEM users”). All it requires is an RNAseq dataset (either fasta or fq format) and a reference transcriptome that it can be aligned to.

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