Transcript Id conversion
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3.9 years ago

Hi i have some transcript id like ENSCAFT00000059187.1 ENSCAFT00000059235.1 ENSCAFT00000059242.1 ENSCAFT00000059247.1 how can i get the gene symbol from these ids......

thanks in advances

gene rna-seq • 3.1k views
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More details will be easy to give some solution. What is your organism (assuming dog) and how did you get those ids ?

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3.9 years ago

Ensembl BioMart instructions might help you: http://www.ensembl.org/Help/Faq?id=125

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3.9 years ago
EagleEye 6.8k

Example from BioMart, I hope this link works. Click the Results tab from top-left.

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3.9 years ago

The four example genes you posted are lincRNAs that don't yet have gene IDs. In general, you can do what Alex Reynolds suggested and use Ensembl biomart.

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As an aside, the "URL" function on Ensembl biomart doesn't seem to work at the moment (otherwise I would have linked to the results). I've reported the issue.

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3.9 years ago

In R, for mapping ensembl transcript IDs to ensembl gene ID and gene symbol: 1) Install EnsDb.Hsapiens.v86 2) Run following command for a transcript in TP53 gene: select(EnsDb.Hsapiens.v86, columns = c("ENTREZID","GENEID", "GENENAME"), keytype = "TXID", keys=c("ENST00000617185"))

However, your transcripts are non coding RNAs and belongs to dog (C.fa). They may not have gene IDs mapped (in ensembl). (as mentioned abvoe) in EnsDb.

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3.9 years ago
mks002 ▴ 190

g: Profiler will be quite useful for Gene ID conversion. This might work out for you.

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