RSEM Prepare Reference - transcriptome instead of genome reference?

Question

[tea.vuki]

Hello,

What is the point of RSEM Prepare Reference tool? I get that it takes standard FASTA reference and standard GTF file to output what? Transcriptome instead of genome reference?

[iraun]

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

[tea.vuki]

Sorry, it is a bit confusing. I don't understand what output of RSEM Prepare Reference actually contains?

[iraun]

Index files of the genome that rsem needs to calculate the expression afterwards.