GO and KEGG analysis

1

Dear Sir/ Madam,

I am doing RNA seq analysis on several studies, I have several questions about GO analysis and KEGG:

  1. What are gene categories? How can I prepare it?
  2. As for selecting a genome ID, I am working on plants and fungi whose genome ID is not available in the galaxy in goseq, and I could not find any possibilities in this tool to upload their IDs, so what could I do?
  3. I have several studies, each study containing 3-4 treatments. I would like to perform DEseq on each treatment of these studies, then merge the DEseq output of these treatments (to get one DEseq for each study), and at the end merge the output of the previous merge of every study together, are there any possibilities in Galaxy to do it? Actually, I am doing analysis like metagenomics but my data are not as many as metagenomics, but I still have different studies containing different treatments that I need to merge and then GO analysis,… I looked for MetaDe in galaxy but I could not find it. If there are such a kind of tools in galaxy for my aim I would appreciate it if to introduce them to me and give me some instructions about them

Thank you very much,

M

2

Hi @MMM
I see you’ve sent the same questions to Galaxy Australia support. I will close the ticket with Galaxy Australia support, because this forum is a better place for questions like yours.

  1. GO categories are controlled vocabulary assigned to genes. Check links in this tutorial for additional information: 3: RNA-seq genes to pathways
    Multiple services are available online, e.g., DAVID, ShinyGO, g:Profiler. GO analysis can be performed locally using R. All options I am familiar with, work on a species level. With these options you will have to analyze plant and fungus data separately.
  2. Practically all mapping tools (aligners) can handle custom reference genomes. Upload genome assembly sequence into Galaxy, and during job setup change source of reference genome to “from history”. It is the top option in HiSAT2 job setup page.
  3. You can run multiple comparisons within a single limma-voom job. See 2: RNA-seq counts to genes for additional information. One of the runs was submitted with two contrasts.

Galaxy tool shed is a software repository for Galaxy. Check if it has the software you are interested in. Many Galaxy servers install tools on user demand.
Kind regards,
Igor

1 Like
4

Dear Marzieh,

scroll to the bottom of page during setup of goseq job. The description provides an example of Gene categories file:

|ENSG00000162526|GO:0000003|
|ENSG00000198648|GO:0000278|
|ENSG00000112312|GO:0000278|
|ENSG00000174442|GO:0000278|
|ENSG00000108953|GO:0000278|

The tool description also has links to popular GO databases where you can search for species you are interested in. As this issue is outside of Galaxy, people working with this species might provide useful insight on appropriate GO database.

Kind regards,

Igor

5

Dear Igor,

Thank you very much for your reply. I will try to find it.

Concerning my previous question that I would like to analyze multiple data from different studies, I will send a protocol as the attached file, please find it. There is a part RNA-seq meta-analysis, but I could not find this tool in Galaxy, is it still functional, if not, are there any alternative tools for it?

Thank you very much with best,
Marzieh

(Attachment Protocol_RNA-SeqDataAnalysisInGalaxy (1).pdf is missing)