Can we use ensembldb to convert transcriptomic bam to genomic bam?

jorainer / ensembldb

This is the ensembldb development repository.

https://jorainer.github.io/ensembldb

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Can we use ensembldb to convert transcriptomic bam to genomic bam? #152

Open smk5g5 opened 3 months ago

smk5g5 commented 3 months ago

Hi,

I have a bam file (nanopore transcripts) aligned to cdna and I need to convert it to genomic coordinates. Is there a way to use ensembldb to do that? Kindly let me know.

Thanks

jorainer commented 3 months ago

no, sorry, ensembldb can not do that. maybe you can do that with the bamtools or the Bioconductor Rsamtools package?