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Old 06-04-2018, 11:42 AM   #7
arctan
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Location: United States

Join Date: Dec 2017
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Thanks for your reply. Since I am working with bacterial RNA, splicing and introns aren't applicable. I agree with you though for eukaryotes, there can be many reads in introns in Ribo-Zero depleted RNA.

For example, https://www.nature.com/articles/nbt.2972/figures/5 is from a paper which did (among other things) a comparison between poly A-selected and rRNA-depleted libraries, and the main difference was the increased number of reads in introns.

However, since I am not working in a species with introns, I think it is more likely that contaminating genomic DNA is the problem. I am doing some tests with additional DNase treatments.
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