does RSEM need STAR?

Question

[Francois Piumi]

Hi, I'd like to estimate gene and isoform expression levels from RNA-Seq data with RSEM. Can it work alone (rsem-prepare-reference and rsem-calculate-expression) or does it need to be associated with the STAR aligner? in other words do I have first to produce bam files with STAR ans then perform a rsem-calculate-expression? Thanks!

[brunobsouzaa]

See here

[Ram]

You'll need to point RSEM to either STAR or bowtie - it will then use that aligner before calculating expression.

Answer 1

[swbarnes2]

You can give RSEM a properly made transcriptome bam to work on. You'll have to use something to make that bam, but STAR designed its transcriptome output to work with RSEM.