Qualimap: intronic reads
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This is due to a combination of pre-mRNA, intron inclusion, and unannotated exons.
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Devon Ryan
There can be, particularly if there's a large degree of variability between the samples.
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Devon Ryan
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How about intergenic reads? Why is it bad to have 50% intergenic reads?
Perhaps this wasn't polyA enriched, in which case that would be quite reasonable.