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thelovelab / tximeta

Transcript quantification import with automatic metadata detection
https://thelovelab.github.io/tximeta/
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Keeping transcript and gene information in the same object - gencode #10

Closed sorjuela closed 5 years ago

sorjuela commented 6 years ago

Hi, I'm using Gencode reference files to makeLinkedTxome and run tximeta. My problem is that after running tximeta I only get transcript information (tx_id) in rowData, but I also want the gene information. This doesn't happen with Ensembl reference files though, meaning in rowData you keep both tx_id and gene_id. So maybe this is a Gencode problem?

mikelove commented 6 years ago

The difference is that Ensembl GTFs are brought in by tximeta with ensembldb (pkg specially designed for these files) while the Gencode GTFs are brought in with GenomicFeatures. So it’s upstream of tximeta in that sense, but this sounds like a very good feature to add to tximeta for Gencode. I’ll work on it when I get a chance. For now, I think you can add them easily with addIds(), although cleaner would be to grab them from the GTF on import.

mikelove commented 5 years ago

Seems to be addressed by Charlotte's commit