Annotation for "upregulated" genes
Hello, I'm a very beginner at NGS.
I ran RNA-seq and performed De Novo Assembly & RNA-seq analysis using CLC Genomics Workbench. The plant material was a non-model species so I used the newly-assembled contigs as reference when running RNA-seq.
I wanted to find out the differentially-expressed genes (or more precisely, contigs) between two libraries; control vs. stressed.
I could obtain the "expression values" for each contigs after RNA-seq analysis, and now I want to know which GO categories they belong to. I was thinking of using BLAST2GO for this purpose, but I didn't know how to extract "up- (or down-) regulated contigs from the contiglist.
Do anyone know how we can extract desired contigs from the contiglist of CLC Genomics Workbench? Any advice will be appreciated.
niwa
I ran RNA-seq and performed De Novo Assembly & RNA-seq analysis using CLC Genomics Workbench. The plant material was a non-model species so I used the newly-assembled contigs as reference when running RNA-seq.
I wanted to find out the differentially-expressed genes (or more precisely, contigs) between two libraries; control vs. stressed.
I could obtain the "expression values" for each contigs after RNA-seq analysis, and now I want to know which GO categories they belong to. I was thinking of using BLAST2GO for this purpose, but I didn't know how to extract "up- (or down-) regulated contigs from the contiglist.
Do anyone know how we can extract desired contigs from the contiglist of CLC Genomics Workbench? Any advice will be appreciated.
niwa