Dear guys,
Is there an RNAseq workflow that can conveniently run to get the reports for most results, like PCA plot, DE list, and function annotation with the proper setup of the run parameters? This can help a lot when having several RNAseq projects and save time and energy...
Best,
You can start by https://github.com/nf-core/rnaseq
The downstream analyses are not implemented because it is difficult to have a well defined routine.
You may use other pipe that go further but not sure it will be 100% compatible with your data. e.g.: https://github.com/hoelzer-lab/rnaflow
Another alternative (as a very rudimentary stating point) might the proposed workflow from Trinity/Trinotate. Following this, you can basically start with raw RNAseq data and Trinity will take care of quality trimming, assembly, mapping and DE analysis (the latter two points with helper scripts in the trinity toolkit), followed by functional annotation with Trinotate. However, it is very difficult to predefine a workflow because the required bioinformatic tools and they way of analyzing the data depend on many things (such as the studied organisms; model organisms can be analyzed differently than non-model organisms) and for a proper analysis you would have to interact with your data (especially for complex statistical design).
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