I'm not sure what I'm missing, but I'm struggling to find an official
GTF file with RefSeq annotations. I'd like to provide the
GTF to Salmon to get gene-level annotations.
Here's Salmon's help info for
File containing a mapping of transcripts to genes. If this file is provided Salmon will output both quant.sf and quant.genes.sf files, where the latter contains aggregated gene-level abundance estimates. The transcript to gene mapping should be provided as either a GTF file, or a in a simple tab-delimited format where each line contains the name of a transcript and the gene to which it belongs separated by a tab. The extension of the file is used to determine how the file should be parsed. Files ending in '.gtf', '.gff' or '.gff3' are assumed to be in GTF format; files with any other extension are assumed to be in the simple format. In GTF / GFF format, the "transcript_id" is assumed to contain the transcript identifier and the "gene_id" is assumed to contain the corresponding gene identifier.
Here's what I've tried:
- NCBI seems to only provide
GFFfiles. I know you can convert between the two, but that hasn't worked well for me in the past. Both file formats allow a lot of freedom, which makes conversions sloppy. Salmon, specifically, is looking for the
- UCSC provides
GTFfiles from RefSeq, but the
gene_idannotation is identical to the
transcript_idannotation (i.e., it's the NM number). Or maybe there's an option I'm missing.
- Ensembl provides exactly the format and all of the information I could hope for, except the
transcript_idis the Ensembl ID (ENST#), not RefSeq (NM#).
Can anyone tell me how to get a
GTF file with hg38 RefSeq annotations?
--geneMap. They expect
gene_idto contain a "gene identifier". I understand that could be several things, but I would prefer the HUGO symbol, as @IanSudbery suggested. In my perusing, I thing Salmon should probably target the
gene_name, at least how Ensembl formats the GTF. In either case, I'm surprised by @DevonRyan's comment that the
gene_idwould equal the
transcript_id. Not arguing that's the case, but what good does that do anyone?? :-) $\endgroup$
tximport(github.com/COMBINE-lab/salmon/issues/98), which I will use. But this isn't the first time I've "needed" a RefSeq GTF and couldn't find one. Just surprises me, but maybe that indicates I need to assess my approach? $\endgroup$