Open bio-lilin opened 8 months ago
Usually, we do not recommend removing duplicates not only for the spike-in but also for the main genome of interest. However, if the spike-in quality is a concern to you (you may want to check other quality control metrics), you can use the sequencing depth normalization strategy, such as CPM.
Thanks, Ye
Thanks for your reply!
Hello, Thank you for creating this helpful tutorial. I have a question about the duplication in the E. coli genome. When I aligned to the E. coli spike-in genome, I found almost all mapped reads marked duplication. Should I use the number of fragments from the E. coli after removing duplication reads, or the number of all fragments from the E. coli when I calculate the scale factor to normalize my data? Thank you, and look forward to your reply.