Endogenous retrotransposons quantifaction from RNAseq

Question

[mforde84]

Has anyone had any experience quantifying retrotransposons in human RNAseq data, eg., LTRs, ERVs, LINE/SINE and Alu1 group RNAs (including SLNRNAs). Is there a custom annotation available to assess these from raw read or bam files? Someone has suggest duskmasker, though when I used it last I don't remember it actually quantifying low complexity regions, but rather simply masking them to either improve specificity in alignment and additional downstream analyses like variant calling.

Martin

Answer 1

[Devon Ryan]

I've had nice experience with TEToolkit, in particular see my PR to add a TEcount function. That'll give you counts for various levels of TE quantification that you can use in DESeq2 or whatever.

[mforde84]

Cool. Exactly what I was looking for. Thanks man.