Question: Ensembl numbers to gene symbols
0
gravatar for Mickael Di
4 months ago by
Mickael Di30
Belgium
Mickael Di30 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 • 200 views
ADD COMMENTlink modified 4 months ago • written 4 months ago by Mickael Di30
1
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson24k 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 COMMENTlink written 4 months ago by Jennifer Hillman Jackson24k
0
gravatar for Mickael Di
4 months ago by
Mickael Di30
Belgium
Mickael Di30 wrote:

Thanks for your answer. It is really helfull.

Best regards

Mickael

ADD COMMENTlink written 4 months ago by Mickael Di30
0
gravatar for Mickael Di
4 months ago by
Mickael Di30
Belgium
Mickael Di30 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 COMMENTlink modified 4 months ago • written 4 months ago by Mickael Di30
0
gravatar for Mickael Di
4 months ago by
Mickael Di30
Belgium
Mickael Di30 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 COMMENTlink written 4 months ago by Mickael Di30

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 REPLYlink written 4 months ago by jpcourneya20
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