search

JiekaiLab / scTE

MIT License
87 stars 27 forks source link

TE families and classes #23

Closed JihedC closed 2 years ago

JihedC commented 2 years ago

Hi! Thank you for the pipeline, it works really well with my 10X mouse single cell RNA-seq data.

I have a question concerning the downstream analysis, the build you have for the mouse TE contains meta-genes based on the name of the TE such as "IAPEz.int" or "IAPLTR1a−Mm".

I would like to know if you have a solution to show the overall expression of an entire family or class of TE, such as LTR or ERV.

I guess I would require to build a custom index using the column from the class and family rather than name in the bed file. I wanted to know if you have thought of that feature?

Thanks again!

jphe commented 2 years ago

Hi, It's nice to see that scTE is useful for you.

For your question, you can build a custome index as yo suggested. Aternativley, scTE outputs the raw counts of each TE name, if you want to get the expression of one class you can easily sum the counts of all TEs blong to that class in the downstream analysis.

JihedC commented 2 years ago

Okay thanks for the insight :) Just to be sure that I understand, I can make the sum of the TE name for one class and modify the count table obtained at the end of scTE manually?

jphe commented 2 years ago

Yes, you can just simply sum it.