Hi everyone,
I have a question in relation to a differential expression analysis that I ran with rRNA contaminated samples.
Essentially, my samples had 60-70% rRNA content, but I chose to go ahead with the analysis once removing these sequences since I had enough reads to work with (15-20M). Contamination was seen in both cases and controls.
However, what I am wondering now is if I can trust the results I am seeing? Is there any way that high rRNA content can affect patterns of expression? Comparing results with cases and controls with no contamination I see 1. More DEGs in the non-contaminated sample 2. Different DEGs (only 1 gene overlap). Of course they are different people but they do have the same disease and the controls are matched so I am a bit at a loss to whether this makes sense
Hope this was clear.
Many thanks.
I have a question in relation to a differential expression analysis that I ran with rRNA contaminated samples.
Essentially, my samples had 60-70% rRNA content, but I chose to go ahead with the analysis once removing these sequences since I had enough reads to work with (15-20M). Contamination was seen in both cases and controls.
However, what I am wondering now is if I can trust the results I am seeing? Is there any way that high rRNA content can affect patterns of expression? Comparing results with cases and controls with no contamination I see 1. More DEGs in the non-contaminated sample 2. Different DEGs (only 1 gene overlap). Of course they are different people but they do have the same disease and the controls are matched so I am a bit at a loss to whether this makes sense
Hope this was clear.
Many thanks.
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