Genome to transcript does not give correct transcript position number

[vetmohit89]

Hello,

I am using genomeToTranscript function to convert genomic sites (positions) to transcripts position.
edbx_1 <- EnsDb.Hsapiens.v86
gnm_tx <- genomeToTranscript(dd, edbx_1)

But when I checked transcript positional data in reference fasta file. I do not see correct bases at the sites this tool generated from genomics sites.

Genome referece: GRCh38.p13

Please help.

Thank you
Mohit

[jorainer]

can you please provide a reproducible example so that I can check the code and result (e.g. what is the dd variable)?

one possible explanation is that you used different versions of genome/transcript databases? The EnsDb.Hsapiens.v86 provides gene/transcript/protein annotations from Ensembl release 86 - so you would need to check and use the correct versions at the genomics sites as well as of the reference fasta file.