Question: RSEM BAM outputs, which one to use for RSeQC?
gravatar for Freek
2.0 years 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 • 785 views
ADD COMMENTlink written 2.0 years ago by Freek10

Did you ever find the answer to this question? I have been used genomic BAM files when processing data through RSeQC, but I wanted to double check whether this was the correct approach.

ADD REPLYlink written 7 months ago by benpkeith10

Hi, thanx for coming back at this. 16 months later, 16 months wiser :)

I use the genome BAM file, although I never tested the transcriptome BAM file, I'm assuming, since the transcriptome BAM was created with the transcriptome as a reference, that there are no reads mapped to anything other than exons (valid transcripts) in said BAM file, this would mean that RSeQC can not determine the number of intronic reads or reads on intergenic regions etc. Since RSeQC uses it's own gene/transcript definitions (I downloaded the BED file they offer), I think it only makes sense to apply RSeQC to a genome BAM.

Still, I might just feed RSeQC the transciptome BAM once and see what happens, in the days to come :)

ADD REPLYlink modified 7 months ago • written 7 months ago by Freek10
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