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mhammell-laboratory / TElocal

A package for quantifying transposable elements at a locus level for RNAseq datasets.
GNU General Public License v3.0
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Normalisation methods #48

Open anna-elisabet opened 2 weeks ago

anna-elisabet commented 2 weeks ago

Hello,

I have performed TElocal for many different samples across 3 tissue types. My next task is to assess the correlation in read count number between TEs and genes. Before I can do this, I need to normalise the read counts. I was thinking I need a normalisation method that would account for differences in "gene length" (also considering the differences in length between genes and TEs), since I will compare read counts within tissue type, not across tissue types.

Let me know if you have recommendations regarding this. Thank you.

olivertam commented 2 weeks ago

Hi,

Thank you for your interest in the software. We don't have a lot of experience in this, but one approach could be to take the length of the TE instance length as the equivalent "gene length" for TE, and process them as you would for RPKM/FPKM approaches. If you need the genomic coordinates (and thus length) of the TE instances in our pre-built indices, they are available here.

Let us know if there's anything else we can help with.

Thanks.