Question: (Closed) Why gene counts from RNA STAR don't match total uniquely mapped counts
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6 months ago by
Qiagen Sciences - Frederick Maryland
daniel.kim30 wrote:


I used RNA STAR to map my reads for a stranded-RNAseq library. Within RNA STAR, i turned on the option to include gene counts and so I included an hg38 GTF file from UCSC table browser. RNA STAR said that of my 20 million total reads, 86% uniquely map (so 17 million reads uniquely mapping), however, when I take the sum of all the gene counts that RNA STAR outputs, it only adds up to 5 million reads. My question is how come the total sum of all the gene counts doesn't add up to 17 million reads and why is it only 5 million? Considering that I'm using RNA STAR to do both the alignment and gene counting I thought they should be concordant.


rna-seq alignment galaxy • 196 views
ADD COMMENTlink written 6 months ago by daniel.kim30


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ADD REPLYlink written 6 months ago by Jennifer Hillman Jackson25k
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