How to assign gene names to ensembl IDs if species not in Biomart

Question

[bioinfo]

Hello,

I would like to align my data to bGalGal1.pat.whiteleghornlayer.GRCg7w. I found the link on ensembl so I already made my index for kallisto.

After mapping I normally use biomart to assign gene names to the Ensembl IDs. However, I don't think that this species is in biomart. When I do searchDatasets(mart = ensembl, pattern = "gallus") I only find the bGalGal1.mat.broiler.GRCg7b version in biomart. Is there any other way I should look for it in biomart?

Otherwise how can I assign gene names to the Ensembl IDs? Would using the gtf file from Ensembl work for that?

Thank you

Answer 1

[GenoMax]

Get https://ftp.ensembl.org/pub/current_gtf/gallus_gallus_gca016700215v2/Gallus_gallus_gca016700215v2.bGalGal1.pat.whiteleghornlayer.GRCg7w.110.gtf.gz and parse names out.

[Ben_Ensembl]

Genomax is exactly right. Just for further context, the annotation for bGalGal1.mat.broiler.GRCg7b is the only chicken annotation available in Ensembl BioMart.

[bioinfo]

Thank you. I ended up using that gtf file, the t2g.py file from https://github.com/pachterlab/kallisto-transcriptome-indices/releases and tximport to assign the gene names.