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Gaius-Augustus / BRAKER

BRAKER is a pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET/EP/ETP and AUGUSTUS in novel eukaryotic genomes
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My long read RNA-Seq was from Nanopore, I was wondering how can i run braker with it. #567

Closed Catherine9826 closed 1 year ago

Catherine9826 commented 1 year ago

I only saw the protocol for integration of assembled subreads from PacBio ccs sequencing in combination with short read Illumina RNA-Seq and protein database, i don't know whether it can works with my nanopore RNA-seq. Or can i list short read Illumina RNA-Seq and long read RNA-Seq together liike: --bam=shortread.bam,longread.bam?

Thanks for your answer.

KatharinaHoff commented 1 year ago

You can of course provide the combined list of bam files. However, this uses only the intron information from RNA-Seq. Whether it makes sense to call genes in the assembled transcripts probably depends on the sequencing error rate. If it's low error rate, it will probably work very well. If not -> not. There were several recent updates by Oxford Nanopore, so I am not sure how your error rate is...

On Fri, Feb 3, 2023 at 9:13 AM Catherine9826 @.***> wrote:

I only saw the protocol for integration of assembled subreads from PacBio ccs sequencing in combination with short read Illumina RNA-Seq and protein database, i don't know whether it can works with my nanopore RNA-seq. Or can i list short read Illumina RNA-Seq and long read RNA-Seq together liike: --bam=shortread.bam,longread.bam?

Thanks for your answer.

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