Hi all friends,
I'm doing RNA-seq analysis for an organism with the sequenced genome, I want to do differential expression analysis at the transcript level and also examine alternative splicing events. Based on enter link description here, I used STAR (instead of HISAT) for mapping, then Stringtie, and now for ballgown, I'm not totally sure about it as the original paper has just 3 citations since 2014. Could you please tell me your experience with this package, how results are accurate and reliable in your hand? Please let me know if you have any suggestion for an alternative package?