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GoekeLab / bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data
GNU General Public License v3.0
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singe exon transcript strand cDNA versus direct RNA nanopore protocol #409

Open tderrien opened 5 months ago

tderrien commented 5 months ago

Hello,

Thank you for providing such a great tool!

For single exon gene/tx reconstructed by bambu, I was expecting them to be unstranded with the cDNA protocol (which is the case) but correctly stranded with the direct RNA protocol (stranded protocol). However, it does not seem to be the case. Could you help to clarify this, please?

We are using bambu version bioconductor-bambu:3.0.8--r42hc247a5b_0

All the best,

Thomas

andredsim commented 5 months ago

Hi Thomas,

Bambu currently doesn't autodetect the protocol used so I need to check if you set stranded=TRUE when running Bambu? I also want to ask what the use case is searching for single exon genes/txs, ie which organism are you in, are you expecting novel single exons? We find they are currently quite a challenge for us, and is something we want to improve further in the future. The results we show in the manuscript are for spliced transcripts and we do see a performance drop for single exon transcripts.

Kind Regards, Andre Sim

tderrien commented 5 months ago

Ty for your quick reply and the useful informations! We will test the option stranded=TRUE (sorry, we missed it). Indeed, most of the novel gn/tx are single exon ones and they are challenging to validate. We are working on ≠ organisms (human, dogs, drosophila...)