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- It needs information about our genome, particularly length of genes. This is available in a particular bioconductor package for many model genomes.
- If your genome is not one of the genomes supported by that package, you can attempt to create the requeired files about your genome using commands mentioned in the goseq manual.
- goseq can also be used to identify enriched pathways, like KEGG pathways
What are your other options?
If you are trying to find enriched GO terms using a list of novel transcripts, BLAST2GO, AmiGO
Web services like DAVID
Get set up
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Make sure you are in the right location cd $SCRATCH/my_rnaseq_course/cuffdiff_results |
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