Question: RSEM BAM outputs, which one to use for RSeQC?
gravatar for Freek
4 months ago by
Freek10 wrote:


I have used RSEM to estimate Transcript abundances in a sample. RSEM uses STAR to do the mapping (if asked) and optionally can output a BAM file where the reads are aligned against the genome and not the transcriptome (this genome file ends in .STAR.genome.bam and is generated with the option "--star-output-genome-bam "). Now I was wondering, I want to use RSeQC to look at various quality related aspects of my BAM file, but which one should I use as input? The one aligned against the transcriptome (.transcript.bam) of the one aligned against the genome (.STAR.genome.bam)?

Highest regards,


rseqc rsem star bam • 187 views
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