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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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Question about the TE expression at the locus level #23

Closed QianzhaoJ closed 1 year ago

QianzhaoJ commented 1 year ago

Hi,

Thanks for developing so helpful tools for transposable element expression at different levels. I have successfully run TElocal to quantify transposable element expression at the locus level, but I still fell confused about the output files. The output of TElocal looks like raw read counts in different TE locus, but if I have multiple samples, with different sequencing depth, are these output files comparable to each other? Maybe I need some normalization for raw read counts? Is it feasible to use FPKM or TPM normlization? or DESeq2 rlog normlization? Thanks in advance!

Best wishes, Qianzhao

olivertam commented 1 year ago

Hi Qianzhao,

Yes, the output is raw read counts in different TE locus. In order to compare between multiple samples, you will need to use a differential analysis software (e.g. DESeq2 or edgeR). What you would do is to join the individual TElocal output, and then feed it into DESeq2 or edgeR. They should be able to normalize the libraries (either ratio of medians or TMM) to do differential analysis. You can then do rlog/vst normalization if you want to visualize the data. I don't think FPKM or TPM normalization is typically recommended for comparing samples, but might be useful for assessing baseline expression within a library (intra-library comparison) Hope this is helpful.

Thanks.

QianzhaoJ commented 1 year ago

I got it! Thank you for your prompt reply.