Question: Why gene counts from RNA STAR don't match total uniquely mapped counts
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8 days 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 • 42 views
ADD COMMENTlink modified 7 days ago by Devon Ryan1.9k • written 8 days ago by daniel.kim30
gravatar for Devon Ryan
7 days ago by
Devon Ryan1.9k
Devon Ryan1.9k wrote:

Many alignments in your dataset aren't to genes, but rather intronic or intergenic regions. Those can't be in the counts but can still align uniquely.

ADD COMMENTlink written 7 days ago by Devon Ryan1.9k

Hi Devon,

This is RNAseq data not DNAseq. Using Agilent Universal Human Reference RNA that has undergone additional DNAse treatment so it can't be from DNA.

ADD REPLYlink written 7 days ago by daniel.kim30

Some RNA-seq reads will map to non-transcript/gene defined regions on the genome.

ADD REPLYlink modified 6 days ago • written 6 days ago by Jennifer Hillman Jackson25k
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