fastqc - typical for Illumina seq?
I read everywhere that you can't just fully rely on the fastqc report while looking at your reads and that this depends on the experiment you are working with. Well in my case the reads were generated using IlluminaSeq. What do I expect as normal when looking at the fastqc.html?
I've asked this question here and I got this link as tip:
But It still doesn't answer my question.
This is what I get:
Well in my case the reads were generated using IlluminaSeq. What do I
expect as normal when looking at the fastqc.html?
Well, for short reads like those you used here (~75nt), I would expect better quality in the 3p end (~28 or higher) because it is what you expect when everything runs smoothly:
RNA quality (RIN>=8, 260/280 ~2, etc)
library prep controls
Nonetheless, if the QC doesn't look ok to you, you can always trim/filter your sequences.
They may also lead to increased false-positive variant calls,
resulting in inaccurate conclusions.
Not necessarily, it depends on many variables, including the coverage.
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