Question: does RSEM need STAR?
0
gravatar for Francois
9 weeks ago by
Francois0
INRA
Francois0 wrote:

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!

rsem • 165 views
ADD COMMENTlink modified 9 weeks ago by swbarnes29.4k • written 9 weeks ago by Francois0

See here

ADD REPLYlink written 9 weeks ago by brunobsouzaa490

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

ADD REPLYlink written 9 weeks ago by _r_am32k
0
gravatar for swbarnes2
9 weeks ago by
swbarnes29.4k
United States
swbarnes29.4k wrote:

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.

ADD COMMENTlink written 9 weeks ago by swbarnes29.4k
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