Question: Clusterprofiler with a set of GO Terms
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gravatar for babji2318
8 months ago by
babji23180
babji23180 wrote:

I work with a species that is not well annotated and hence I made a trinity assembly on my own and did the analysis. I am looking at a set of 1000 genes that I am interested in profiling. I did a local blast and annotated the genes using Blast2GO. Is there a way I can visualize a list in the format shown below. I am trying to use clusterprofiler but I am not sure on how to import a file of this format for use with the r package. Could you tell me if this is possible in clusterprofiler. Format:

Trinity ID GO Term

TRINITY_DN6109_c0_g2_i2 GO:0003723; GO:0003735; GO:0006412; GO:0015935

TRINITY_DN943_c0_g1_i2 GO:0000228; GO:0003723; GO:0003735; GO:0005730; GO:0006412; GO:0022627

TRINITY_DN6271_c3_g1_i2 GO:0003746; GO:0003924; GO:0005525; GO:0006414

TRINITY_DN9010_c0_g5_i1 GO:0003735; GO:0005840; GO:0006412

TRINITY_DN3760_c2_g3_i2 GO:0003735; GO:0005840; GO:0006412

Thanks

ADD COMMENTlink modified 8 months ago • written 8 months ago by babji23180

If you use Blas2GO you can also download the GO id correspondence to make a barplot on your own or using the function graphs.

ADD REPLYlink modified 8 months ago • written 8 months ago by Buffo1.7k
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