Question: Clusterprofiler for KEGG enrichment (non-model species)
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gravatar for sbchua.1990
4 months ago by
sbchua.199010
sbchua.199010 wrote:

Hi, I wish to use clusterProfiler for KEGG pathway enrichment (non-model species, Pleurotus pulmonarius). I want to use my whole transcriptome as background. I now have files for whole transcriptome and DEG in the following format:

TRINITY_identifier KO_number

How can I proceed from here? What kind of extra input files are needed?

rna-seq R gene • 319 views
ADD COMMENTlink modified 10 days ago by sutturka100 • written 4 months ago by sbchua.199010

I am not sure for clusterProfiler in particular, but normally if you want to do KEGG or GO analysis with non-model species, you'll first need to know which genes of your mushroom map to which KEGG pathway or GO term. I don't think TRINITY identifiers are sufficient for this purpose.

ADD REPLYlink modified 4 months ago • written 4 months ago by b.nota3.6k

Thanks for reply. Ko_number at second column. Do you have any suggestion for suitable software?

ADD REPLYlink written 4 months ago by sbchua.199010

When I worked with non-model species, a decade ago, I used blast2go software for this. But I am not sure if this is still the best approach nowadays (and if it is still free software). I 've been working for too long with model species now.

ADD REPLYlink written 4 months ago by b.nota3.6k
0
gravatar for sutturka
10 days ago by
sutturka100
USA
sutturka100 wrote:

May be this document will be useful.

ADD COMMENTlink modified 10 days ago • written 10 days ago by sutturka100
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