A new Coverage tab directly compare multiple reference assemblies. You can compare different sequencing datasets assembled against the same reference sequence with expression level comparison. Now that you can store multiple assembly jobs in a single Assembly Project, you can also directly compare multiple runs of the same dataset against a single reference sequence to compare which is the best assembly.
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For RNAseq analysis look at the Coverage tab of a contig. This contains very detailed information needed for such analysis such as RKPM and TPM for every feature.