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Question: Ensembl numbers to gene symbols
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gravatar for Mickael Di
11 months ago by
Mickael Di • 30
Belgium
Mickael Di • 30 wrote:

Hello,

I already aks in a post this question:

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?

Jennifer asked me: The tool Join two Datasets side by side on a specified field could be used.....

Can you tell me please: 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.

Thanks a lot

Best regards

Mickael
assign metadata datatype tabular dataset • 376 views
ADD COMMENT • link •
modified 11 months ago by Jennifer Hillman Jackson ♦ 25k • written 11 months ago by Mickael Di • 30

Thanks for your answer Devon. CAn you tell me how can I set as "tabular" datatype in galaxy? I upload a text file and when I want to join the data I cannot select the text file the format was not recognize.

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

Please see: https://galaxyproject.org/support/#troubleshooting > How do I find, adjust, and/or correct metadata?

Thanks, Jen, Galaxy team

ADD REPLY • link written 11 months ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for Devon Ryan
11 months ago by
Devon Ryan • 1.9k
Germany
Devon Ryan • 1.9k wrote:

Text works just fine, you'll just want to ensure that it's set as the "tabular" datatype in Galaxy.
ADD COMMENT • link written 11 months ago by Devon Ryan • 1.9k
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