Do STAR genome index and RSEM reference need to be from same files?

Question

[prabin.dm]

Hi, I am using STAR for read alignment. The STAR genome index was built on .gtf and .fa downloaded from UCSC genome browser.

Should I run rsem-prepare-reference on the same .gtf and .fa files ? Or I can have rsem reference built on gft and fasta files downloaed from different source ?

Answer 1

[grant.hovhannisyan]

In general its a bad idea to use different reference genomes and annotations, there is a very high chance of some downstream incompatibilities. So unless there is a very strong reason you have to use different files, you should go with the same ones.

Answer 2

[WouterDeCoster]

For STAR you use the genome (DNA) and for RSEM you use the transcriptome (cDNA), however, you can also create an index for RSEM using the genome and a gtf of all transcripts.