Which genome index should be used for "rsem-calculate-expression" command after RNA-seq reads mapping with STAR aligner ?
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22 months ago
taoi2 ▴ 30

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 ?

RNA-Seq STAR RSEM • 656 views
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