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
1 answer
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.
Log in to answer this question.
-
Question about assigning gene names, tximport and DESeq2
written by bioinfo •
-
Ensemble Service error
written by anasjamshed
-
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.tx…
written by bioinfo •
-
How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
written by bioinfo •
-
How to assign gene names after kallisto when I add GFP?
written by bioinfo •
-
How do I get estimated gene counts for a reference that contains GFP using Kallisto?
written by bioinfo •
-
Ensembl version for mapping and annotating genes
written by bioinfo •
-
Estimated gene counts with tximport
written by bioinfo •
-
biomaRt does not convert entrez gene id to ensembl gene id
written by Bane •
-
biomaRt not finding all genes
written by danielcgingerich •
