Question: Extract subset (based on GO or KEGG categories) from Trinotate.xls for goseq analysis
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gravatar for sbchua.1990
2.1 years ago by
sbchua.199030
sbchua.199030 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 • 1.2k views
ADD COMMENTlink modified 2.1 years ago by h.mon26k • written 2.1 years ago by sbchua.199030
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gravatar for h.mon
2.1 years ago by
h.mon26k
Brazil
h.mon26k 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 2.1 years ago • written 2.1 years ago by h.mon26k
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