RSEM Prepare Reference - transcriptome instead of genome reference?
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Not sure if I understood the question. The reference fasta you have to provide as input should contain genomic sequences (not transcriptome).
The output will contain the index files rsem needs to quantify the expression. https://deweylab.github.io/RSEM/README.html#built
Sorry, it is a bit confusing. I don't understand what output of RSEM Prepare Reference actually contains?
Index files of the genome that rsem needs to calculate the expression afterwards.