Hi! I recently discovered recount3 and have found it incredibly helpful in finding information and generating hypothesis about particular genes. I also work with so-called "hypothetical transcripts" which are annotated in the RefSeq annotation (please find more information on this page: refseq) which do not exist within the Ensembl/Genecode annotation (I tried searching through the GTF file for the version you listed to see if the genes I'm interested in were present). Do you have any advice for how I could still utilize the data within recount3 to learn more about these "unrepresented" genes? Thank you very much for your help.

(P.S. for additional information I downloaded the Genecode GTF from this website: genecode)

Hi,

You can use megadepth https://bioconductor.org/packages/megadepth to quantify the base-pair expression levels for genomic regions of interest along the hg38 coordinates using the BigWig files provided by recount3. By doing so, you can quantify un-annotated regions of your interest, and annotations we didn't consider in recount3. We actually used megadepth ourselves for building recount3.

Best, Leo