Which genome index should be used for "rsem-calculate-expression" command after RNA-seq reads mapping with STAR aligner ?
After RNA-seq paired-end-reads are aligned with STAR, I want to calculate expression levels using RSEM.
The STAR index was built on .gtf and .fa downloaded from human GENCODE.
Can "rsem-calculate-expression" command be run with both "Aligned.toTranscriptome.out.bam" files from STAR and the above STAR index ?
Or
Must I create an index for RSEM and use the index in stead of the above STAR index ?
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