How do I find which ones are TEs and which are genes?

JiekaiLab / scTE

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How do I find which ones are TEs and which are genes? #84

Open gdolsten opened 2 months ago

gdolsten commented 2 months ago

How do I find which of my adata is a TE and which is a gene? adata.var.index is completely empty THanks, Gabe

jphe commented 2 months ago

How do you bulid the index? if you use the default opition like " scTE_build -g mm10 ", then you can extract the gene name from the ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M21/gencode.vM21.annotation.gtf.gz file, and get the TE name from http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/rmsk.txt.gz file