search

juheon / LRCAGE

MIT License
1 stars 1 forks source link

the question about TE quantification #1

Open songlyzz opened 1 month ago

songlyzz commented 1 month ago

Hi juheon, I have read your recent published paper "Epigenetic therapy potentiates transposable element transcription to create tumor-enriched antigens in glioblastoma cells", it is really solid results for TE specific antigens for tumor. There I have some questions:

1726149113969

I noticed that you normalized the TE for gene's expression, but you do not mention the gene's expression whether normalized for TE. In my opinion, they should nomalize separately. Meanwhile, I did not see the reference of TE's locus refered, I am curious about how many reference TE contain.

Yours sincerely.

juheon commented 1 month ago

Hello,

For TE annotation, we utilized Repeatmasker from the UCSC Table Browser for the hg38 genome assembly.