Question: How to plot NGS data?
7.6 years ago by
Bernd Jagla • 30
Bernd Jagla • 30 wrote:
Hi, I have "a few" reference genomes from NGS resequencing experiments and annotation in GFF format that I would like to use in some of the plotting functions that are available (i.e. geneplotter, ChromHeatMap). Actually, I would to integrate these with expression results from correlated NGS RNA-seq experiments. My overall approach currently includes using BSGenome, GenenicFeature/FeatureDb, expressionSet and geneplotter/ChromHeatMap. I haven't figured out how to fill an expressionSet class with my counts and how to define regions / genes. Also, is this the class to use? There seem to be too many possible routes to go and I am feeling quite lost... I am now in the process of creating a BSGenome object using BSGenomeForge, which seems to be working. As all this seems to be quite complicated and I haven't found a complete guide on how to visualize NGS results I would like to verify this approach by someone and maybe get some pointers to help me on how to do visualization with RNA-seq experiments... Thanks a lot for your kind help and consideration. Bernd,
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