Having a lot of trouble converting Gene Ranges to GeneID.

Question

[James]

I'm having trouble converting gene ranges to gene ids for mm10. For example I have a dataframe of "chromosome", "start", "end", and I want the associated "GENE SYMBOL" for each row. I was looking online, which brought me to GRanges, so I converted the data frame to GRanges objects. I don't really know what to do next.

I was looking at other forums (including this one) and I couldn't find an explicit answer to help me. I'm getting pretty lost. I was looking into some other methods and biomaRt was mentioned. TxDb.Mmusculus.UCSC.mm10.knownGene was also mentioned, but I don't know what to do with these.

Feeling #frustrated, so I appreciate any help.

[barslmn]

Hi, you can look into annotate functions for tools like this. GRanges have such function https://jmw86069.github.io/splicejam/reference/annotateGRfromGR.html

Another alternative bedtools, have a function name intersect https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html. Where you can do an outer join of two files and annotate your interval file with your genome annotation.