In my RNA-seq data, I have on average >70% duplicate read percentage ( for all samples). Any suggestion how to clear my data to eliminate this bias?
You could either remove the duplicates or take a look at the average count/fpkm/tpm value for the duplicated reads.
Rishabh Kulkarni makes a valid point. Eliminating duplication based on your experiment setup is essential for enhancing your experiment's potential. This process is crucial for your RNA seq. It's not about bias; it's about maximizing the impact of your research. Let's ensure you're moving in the right direction with our experiment setup.
Depending on the type of your experiment, read duplication is to be expected and deduplication is not necessarily beneficial. You might want to have a look at this article: https://www.nature.com/articles/srep25533
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