Duplication in E.coli genome

[bio-lilin]

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.

[yezhengSTAT]

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

[bio-lilin]

Thanks for your reply!