Question: Extract subset (based on GO or KEGG categories) from Trinotate.xls for goseq analysis
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gravatar for sbchua.1990
17 months ago by
sbchua.199020
sbchua.199020 wrote:

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?

rna-seq R gene • 849 views
ADD COMMENTlink modified 17 months ago by h.mon20k • written 17 months ago by sbchua.199020
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gravatar for h.mon
17 months ago by
h.mon20k
Brazil
h.mon20k wrote:

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
ADD COMMENTlink modified 17 months ago • written 17 months ago by h.mon20k
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