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Question: How do I obtain gene names from ENSG values?
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gravatar for nrickett
13 months ago by
nrickett • 0
United Kingdom
nrickett • 0 wrote:

Hi

I have performed DGE using DESEQ2 (input htseq-count, following mapping by BWA-MEM) and have ended up with a list of differentially expressed genes in ENSG format. I was hoping there is a way to convert these into the actual human gene names.

Thanks very much for any help.

rna-seq galaxy • 1.1k views
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modified 13 months ago by Jennifer Hillman Jackson ♦ 25k • written 13 months ago by nrickett • 0
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gravatar for Jennifer Hillman Jackson
13 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Three options:

1 - Use a reference annotation dataset in the analysis that includes the target gene names as an attribute. This is "gene_name" if using Cuffdiff and a GTF file; some other tools require gene_id (GTF) or Gene (if in GFF3 format). iGenomes is a good source if your genome/version is included (down the tar file locally, unpack it, then just upload the genes.gtf dataset to Galaxy).

2 - Find a file that maps the two IDs and use the tool Join two Datasets side by side on a specified field. The UCSC tables named like "xref" are one choice (if your genome is supported there): http://genome.ucsc.edu

3 - This will not work for your case, but for others wanting to map IDs, the tool UniProt ID mapping and retrieval is often helpful.

Hope that helps! Jen, Galaxy team
ADD COMMENT • link written 13 months ago by Jennifer Hillman Jackson ♦ 25k
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