I have data from a few RNAseq experiments on a non-model eukaryote, in which I have assembled transcriptomes with Trinity and analyzed expression with EdgeR (after mapping back to the transcriptome).
I've attempted to annotate using both Trinotate, and also Blast2GO. From there, the plan was to use BiNGO, as discussed here.
The plan was to take my GO terms from differentially expressed transcripts and compare that to the background (all of the GO terms from the assembly) to assess overrepresentation of various themes. However, I get no output when I run BiNGO within Cytoscape, using a custom "genome" annotation file (with each line representing a transcript and GO term, with some transcripts being represented by more than one GO term, and hence, more than one entry per transcript) and a list of GO terms from DE genes.
I would appreciate any help with BiNGO (I have attempted e-mail the developer with no reply), or with any recommendations for appropriate GO analysis!
Thank you,
Anthony
I've attempted to annotate using both Trinotate, and also Blast2GO. From there, the plan was to use BiNGO, as discussed here.
The plan was to take my GO terms from differentially expressed transcripts and compare that to the background (all of the GO terms from the assembly) to assess overrepresentation of various themes. However, I get no output when I run BiNGO within Cytoscape, using a custom "genome" annotation file (with each line representing a transcript and GO term, with some transcripts being represented by more than one GO term, and hence, more than one entry per transcript) and a list of GO terms from DE genes.
I would appreciate any help with BiNGO (I have attempted e-mail the developer with no reply), or with any recommendations for appropriate GO analysis!
Thank you,
Anthony