I need to detect, quantify, identify differential splicing, and compare the alternative splicing across different RNA seq datasets of plants.
I am the beginer in this field. Please suggest the best pipeline.
Thanks.
Tophat--> Cufflinks (Cuffdif) should work:
http://cole-trapnell-lab.github.io/cufflinks/
A tools that has been used to identify unanotated splicing events for plants and that, in my opinion, gives robust results is SplAdder (See: http://biorxiv.org/content/early/2016/02/05/017095).
In my experience, it is also important that one chooses a good read aligner, e.g. STAR and filters out reads that map to multiple locations, as these can otherwise lead to false positives.
A good description of a pipeline to detect and identify differential splicing events in plants, can be found in: http://www.plantcell.org/content/25/10/3726.short
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Nucleic Acids
- RNA