Extract subset (based on GO or KEGG categories) from Trinotate.xls for goseq analysis

Question

[sbchua.1990]

Hi, I have assembled unigenes using Trinity pipeline and annotated them using Trinotate pipeline. How can I extract a subset of genes (based on GO or KEGG categories, for example oxidoreductases activity) from Trinotate.xls for goseq analysis?

Answer 1

[h.mon]

Using grep:

grep "someGOterm" trinotate.xls

In case you want to filter for several GO terms, put them into a file, one per line:

grep -f GOterm.file trinotate.xls