Is TETranscripts useful for repetitive sequences analysis?

Question

[frarodmar17]

I was analysing repetitive sequences data and I was thinking of using TETranscripts because it deals really good with multimapped sequences, but I am not sure if it is really specific por transposons. Is this software able to identify other types of repetitions? I was thinking of using this gtf annotation file: https://www.dropbox.com/scl/fo/o0my0l1c7s40un9qv6yvf/AHc6QEU_oIS3v32vgmXAUIM/GRCh38_Ensembl_rmsk_TE.gtf.gz?rlkey=sbsb00bbcrq4ofmq1oviy7ws1&dl=0

[GenoMax]

I was analysing repetitive sequences data

Can you clarify what kind of analysis you are looking to do?

[frarodmar17]

I am looking for all types of repetitive elements in RNA: LTRs, LINEs, SINEs, satellites, microsatellites, etc.

Answer 1

[Michael]

TEtranscripts is for differential expression analysis of transposable elements. This works only for elements that are transcribed as RNA or have an RNA intermediate. So likely no luck with satellite sequences.

[frarodmar17]

But satellites can also be transcribed. I do not know if TETranscripts is specific for RNA repetitive sequences or only for RNA transposons?

[Michael]

I have only used this once, but I think the inclusion of any element depends on whether it is present in the GFF file. If the region has coverage, it should be included.