Question

Qualimap: intronic reads

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5.5 years ago

RiNG ▴ 10

I am using qualimap to assess the quality of my alignments.

However for most samples I am having around 12% of intronic reads. I know for a fact I have no gDNA contamination. What is causing this to happen?

alignment • 1.5k views

ADD COMMENT • link 5.5 years ago by RiNG ▴ 10

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How about intergenic reads? Why is it bad to have 50% intergenic reads?

ADD REPLY • link 5.5 years ago by RiNG ▴ 10

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Perhaps this wasn't polyA enriched, in which case that would be quite reasonable.

ADD REPLY • link 5.5 years ago by Devon Ryan 104k

score 3 · Answer 1 · 2018-10-02

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5.5 years ago

Devon Ryan 104k

This is due to a combination of pre-mRNA, intron inclusion, and unannotated exons.

ADD COMMENT • link 5.5 years ago by Devon Ryan 104k

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Is there a correlation between this and the lack of sample clustering in a PCA plot?

ADD REPLY • link 5.5 years ago by RiNG ▴ 10

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There can be, particularly if there's a large degree of variability between the samples.

ADD REPLY • link 5.5 years ago by Devon Ryan 104k