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JiekaiLab / scTE

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only TE analysis #24

Closed JihedC closed 2 years ago

JihedC commented 2 years ago

Hi ! I have another question.

In the Figure 1e of your article, I understood that you performed a downstream analysis only based on the expression of TE. Does it mean that you filtered the count table you got after running scTE to maintain only the rows with TE name (and exclude genes) before performing the downstream analysis (Scanpy/Seurat)?

Thanks for your answer!

Jihed

jphe commented 2 years ago

Hi Jihed,

Yes, we just seperate TEs and genes in the downstream analysis as you suggested.

For detail please refer to this: https://github.com/jphe/scTE/issues/3

Jphe