I am doing Isoform switch prediction studies from differential data using IsoformSwitchAnalyzeRhttps://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/isoformswitchanalyzer/SA9sJCQXM54/eNxVps5pDAAJ. The error retrieved :- " you have NOT been doing transcript reconstruction/assembly with Cufflinks/Cuffdiff. If you have not reconstructed transcripts we receomend to use Kallisto or Salmon to do the quantification instead - they are more accurate and have better biase correction methods."
The reason behind seems to be not using Tophat2 --> cufflinks -->cuff merge -->cuffdiff -->IsoformSwitchAnalyzeR, because the pipeline I have followed is STAR -->cuffdiff -->IsoformSwitchAnalyzeR
Should I follow former workflow for Isoform switch analysis or later can also work with some additional efforts? Please comment/suggest.