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Old 04-03-2018, 09:38 AM   #6
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Originally Posted by AlexCalderwood View Post
They were made using "NEB next ultra directional library kit", which uses dUTP method to retain strandedness, and should give an insert size of ~200bp
Okay, then my hypothesis is that the reverse read is always reading 5' in the cDNA of the forward read. So that elevated AT% is just polyA tail. Or, since you mention hits to "predicted genes", the elevated AT% may just be 3' or 5' non-translated. (Not sure which orientation the NEB kits retain.) Nor whether a 5' or 3' bias is likely in your sequence.

The non-translated regions of plants are often replete with transposable elements which can themselves have lower GC content. Or, with time after insertion, often become reduced in GC due to cytosine methylation. That is, C deamination is easily repaired because "U's" don't belong in DNA. However, 5-me-C deaminates to "T". So, over evolutionary time, simply methylating transposable elements has a sort of slow-motion "RIPping" effect.

Just speculation on my part, of course.

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