I am working on a virtual project for WGS combined with RNA seq for annotation. The RNA will be sequenced using PacBio Isoseq (Sequel II, HiFi-reads). With some research, I found that StringTie2 is useful for this. In their release paper , they sometimes mention previous alignment or mapping with TopHat or minihat, but I don't find a manual where they say the same. Now I don't know what is supposed to be the input of StringTie2: raw RNA reads, or a mapped BAM-file?

Thank you!

  • $\begingroup$ What exactly is unclear after reading the manual: github.com/gpertea/stringtie It is mapped reads that are input. I do not know what minihat is, you probably mean minimap2, which is probably a good choice for long reads. For sure don't use tophat. It is old and deprecated, for short reads use something like STAR or hisat2. $\endgroup$
    – user3051
    Dec 26, 2020 at 11:43
  • $\begingroup$ I was not sure if StringTie2 has the same requirements, but ok, it's clear that I should use mapped reads. I indeed meant minimap2, must've confused it with tophat ;) Thank you! $\endgroup$
    – WilGos
    Dec 26, 2020 at 13:44


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