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comprna / RATTLE

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing
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Combine IsoSeq and transcripts from de novo annotation? #28

Open Adamtaranto opened 2 years ago

Adamtaranto commented 2 years ago

Hi,

Is there a sensible way to combine IsoSeq flnc reads and predicted transcripts from an older genome annotation using RATTLE? I expect that the ISoSeq dataset will contain transcripts from genes missing in the draft genome, and also that the de novo annotation will contain genes that are no expressed in the iso-seq samples. I'd like to try to capture the maximum diversity of transcripts/genes for an RNA-Seq DGE experiment.

Thanks, Adam

EduEyras commented 2 years ago

Hi,

You could perhaps pool them together and analyse them with the third step in RATTLE. This is the transcript polishing step, and it aims to eliminate possible redundancy in the transcripts built in the previous steps.

You could also run RATTLE from the initial step, modifying the parameters so that clusters are formed with fewer transcripts (default is >5 reads) and perhaps also imposing more stringent parameters for matching, especially similarity score 1, since you expect your input sequences to have higher sequence quality.

I hope this helps

cheers

Eduardo

On Sat, 2 Oct 2021 at 12:47, Adam Taranto @.***> wrote:

Hi,

Is there a sensible way to combine IsoSeq flnc reads and predicted transcripts from an older genome annotation using RATTLE? I expect that the ISoSeq dataset will contain transcripts from genes missing in the draft genome, and also that the de novo annotation will contain genes that are no expressed in the iso-seq samples. I'd like to try to capture the maximum diversity of transcripts/genes for an RNA-Seq DGE experiment.

Thanks, Adam

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