What Tool Are You Using for Transposable Elements Analysis
I intend to account for transposable elements in my mapping and quantification process. Specifically, I was hoping for a tool that does quantification at the locus level for multi-mapped reads. I want something that is compatible with Python 3 for mamba and Conda. What tools are you using?
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SQuIRE is pretty good at what you are looking for. It quantifies both at locus and sub-family level. It also handles multi-mappers nicely by employing EM (expectation-maximization) algorithm.
Here is the github page:
And here is the paper: