How to Add gene information (gene name, strand etc.,) to the DESEQ2 output file generated by Galaxy

#1

Dear Admin,

I would like to add gene information (gene name, strand, transcript IDs, uniprot IDs etc) to the DESEQ2 output file generated by Galaxy (EU).
Please check the attached slide picture.

Is there a way to create it using tools in galaxy or using R ?

GALAXY%20QUESTION
GALAXY QUESTION.png960x720 344 KB

.

Thanks in advance.
James PC

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#2

Dear James,
You can use https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/iuc/deg_annotate/deg_annotate/1.0 for this purpose. At the moment, it can add gene position, gene symbol and biotype from a GTF file but not uniprot, pathways and GO terms.

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#3

Hi Pavan, Thank you very much for the input. It worked.

image
image.png1921×916 199 KB

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#4

While extracting Workflow, recently i get this error multiple times.
Could you tell what might be the reason ?

image

#5

Hi Pavan,

Sorry, I found the issue, removed a partially deleted file from cutadapt step, it worked. Thank you.
Happy New Year Galaxy folks.

Regards,
PC

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