Ensembl numbers to gene symbols

Question: Ensembl numbers to gene symbols

11 months ago by

Belgium

Mickael Di • 30 wrote:

Hello, I performed RNA Seq analysis using DeSeq2. At the end of the analysis it got differential expression of genes associated with Ensembl numbers. My GTF is annotated with Ensembl numbers.

ENSMUSG00000026879 ENSMUSG00000026043 ENSMUSG00000092609 ENSMUSG00000018830 ...

I am wondering: how can I join this Ensembl numbers to Gene symbols after DeSeq2 analysis and get a text file with ensembl numbers joined to gene symbols? What tool can I use in galaxy in order to join Ensembl numbers to Gene symbols?

Can you explain preciesly if you have information about that?

Thanks for your help

Mickael

ensembl gtf reference gene rna-seq • 495 views

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modified 11 months ago • written 11 months ago by Mickael Di • 30

11 months ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The tool Join two Datasets side by side on a specified field could be used. Input your DeSeq2 results and a tabular mapping file containing the two values. For your case, Biomart would be a good source.

If your final goal is functional information, try the tool David (Database for Annotation, Visualization, and Integrated Discovery).

Galaxy Tutorials: https://galaxyproject.org/learn/

Similiar Q&A can be found in the right sidebar listings >>>

Thanks! Jen, Galaxy team

ADD COMMENT • link written 11 months ago by Jennifer Hillman Jackson ♦ 25k

11 months ago by

Mickael Di • 30

Belgium

Mickael Di • 30 wrote:

Thanks for your answer. It is really helfull.

Best regards

Mickael

ADD COMMENT • link written 11 months ago by Mickael Di • 30

11 months ago by

Mickael Di • 30

Belgium

Mickael Di • 30 wrote:

Please another question: what should be the format of the tabular mapping file? .txt does not work so .gtf, .other format? What tool can I use to convert my .txt fie into .other format in galaxy? Thanks for your answers.

Mickael

ADD COMMENT • link modified 11 months ago • written 11 months ago by Mickael Di • 30

11 months ago by

Mickael Di • 30

Belgium

Mickael Di • 30 wrote:

Mickael

ADD COMMENT • link written 11 months ago by Mickael Di • 30

Mickael, a text editor like Atom or Visual Studio code is handy to run along side while working with Galaxy to open up a .txt file and change it to a number of different formats like csv or tsv. Then you can re upload it to galaxy. Hope that may help.

ADD REPLY • link written 11 months ago by jpcourneya • 20

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