Quantification of Transposable elements and/or chimeric TE-gene splice variants

[Kiliankleemann]

Dear Bambu team,

thank you making such an amazing tool available!!
I was wondering if you have come across and/or thought about how bambu could be implemented to quantify the transcription of transposable elements?

I would greatly appreciate hearing your thoughts and suggestions.

Kilian

[andredsim]

Hi Kilian,

Yes Bambu should be able to be used to identify and quantify transposable elements. In our paper we used Bambu to quantify isoforms from repetitive HERVH-LTR7 retrotransposons in human embryonic stem cells. Some points to consider are if you are looking for non-spliced TEs you will need to set opt.discovery = list(min.txScore.singleExon = 0) or some value < 1 to ensure bambu will report them. Also Bambu uses which ever alignment is provided and ignores secondary alignments, so if there are 2 very highly similiar TE's in your sample, the aligner may make mistakes there.

Hope this helps,
If you have further questions feel free to ask, but I will close this for now.

Kind Regards,
Andre Sim

[Kiliankleemann]

Hi Andre, thank you so much for the info! I will check it out. Regarding the Secondary alignments: You're saying that multi-mappers will not be account for?
Kind regards Kilian

[andredsim]

Hi Kilian,

Correct, bambu will use the primary alignment which should generally be the highest scored alignment across multi-mapping possibilities. Supplementary alignments are still used and are treated as separate reads (but this is of less relevance for your use case I imagine)

Kind Regards,
Andre Sim