This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Is TETranscripts useful for repetitive sequences analysis?

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

tetranscripts
• 1,390 views • link
updated by Michael Dondrup Michael Dondrup • written by frarodmar17 • frarodmar17

I was analysing repetitive sequences data

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

• 0 views • link
written by GenoMax GenoMax

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

• 0 views • link
written by frarodmar17 • frarodmar17

1 answer

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.

• 0 views • link
written by Michael Dondrup Michael Dondrup

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

• 0 views • link
written by frarodmar17 • frarodmar17

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.

• 0 views • link
written by Michael Dondrup Michael Dondrup

Log in to answer this question.

More posts like this