Hi @Monish_V
Glad this helped!
And for this part, yes!
Start here → Hands-on: Genome-wide alternative splicing analysis / Genome-wide alternative splicing analysis / Transcriptomics
Then, to review some prior troubleshooting with the details this is a good topic → GTN Transcriptomics Hands-on: Genome-wide alternative splicing analysis. Troubleshooting reference data choices!
Note: limiting the reference data to the primary autosomes chr1-22, chrX, and chrM will yield cleaner results and allow even large mammalian genomes such as human to processing using the public computational infrastructure. You can prepare this data and use it with any tool in Galaxy as custom data inputs (instead of using the default built-in reference genome with the other fragments). More → Reference genomes at public Galaxy servers: GRCh38/hg38 example
A lot of information! The important parts are to plan ahead with the data preparation. Making use of the workflow is another choice – even just to see what it does before tuning with your own tool choices/parameters.
Hope this helps! 