how to get genomic location of transcript positions

Question

[baibhu1234]

I have used your tool m6Anet for the m6A site prediction and found the results.

as the results are with respect to the transcripts position of m6A sites are on the transcripts.

But I want the exact genomic locations of the m6A sites. How can we do that using the gff file? I can see the transcripts length = 5'UTR + CDS's + 3'UTR for each "mRNA" entry in gff file.

I can do for 1-2 transcripts but how to get the genomic location of the sites on each of the transcripts automatically.

[Ram]

your tool m6Anet

Whom are you talking to? If you are looking for the m6anet developers, they ask you to raise an issue/discussion on github: https://github.com/GoekeLab/m6anet?tab=readme-ov-file#getting-help

Answer 1

[GenoMax]

You can take a look at the answers here to convert transcript co-ordinates to genomic coordinates:

Convert transcript coordinates to genomic coordinates
Convert from transcripts coordinates to genomic coordinates in python
How to convert Human Ensembl transcript coordinates to GRCh38