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/
yes the easy one is go for partek flow software
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