FORUMFavorite splice aware alignment program for RNA-Seq?
mattdoug asked 1 year ago



  • TopHat, STAR, HISAT, something else? What program(s) have you used, and did you pick them for a particular reason?

    3 Answers
    zhibin Staff answered 1 year ago



  • I used them all but my favorite becomes hisat recently. It is fast with low memory requirement. I think people use star because of the speed but it uses too much memory. The alignment speed for hisat is compatible with star.

    jflucier Staff answered 1 year ago



  • You could also look at this post that is related to your question:
    https://bioinformatics.computecanada.ca/question/alternative-splicing-detection-in-rna-seq-data/

    jrosner Staff answered 1 year ago



  • You can also have a look at this Nature paper (2013) that takes a deep dive into evaluating various splice alignment tools and this PMC article (2014) that looks at differential splice analysis tools.
    perhaps slightly outdated, but likely still relevant.