I am trying to determine the best RNAseq analysis pipeline to use to identify novel spliceforms (I also care about non-coding RNAs). I have an enormous RNAseq dataset which I have already analyzed using STAR to map and RSEM to quantify. My data is in .fastq, generated from stranded library, ribodepletion method, 60M PE reads/sample, 100bp reads and from mouse. I thought I read that RSEM was not able detect novel spliceforms (am I wrong??). The pipeline I am thinking would work for this is Hisat2 > Stringtie > Ballgown. My questions are: (1) Can I use my current pipeline (STAR > RSEM) to identify novel spliceforms using special run parameters or do I need to redo the analysis with a different pipeline. (2) If a different pipeline would be better for this, which pipeline would people recommend and what options would you use for mapping and quantification.
My boss and I never discussed wanting to identify novel spliceforms and now he has a grant due and wants this data ASAP, so I'm on a timecrunch! Also, I've only been doing bioinformatics for two years and have taught myself, so I apologize if anything doesn't make sense. Please ask for clarification if needed. Your advice is greatly appreciated.