<p>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 <a href="https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1910-1" rel="nofollow noreferrer">release paper</a> , 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?</p>
<p>Thank you!</p>

CC BY-SA 4.0
2020-12-26T13:44:20.127Z
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!
WilGos
<transcriptome><pacbio><stringtie>
Required input files for StringTie2
# Required input files for StringTie2

(Asked by: username_0 on 2020-12-26)

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](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1910-1) , 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!

**Tags:** transcriptome, pacbio, stringtie
> **Comments:**
> **username_0**: 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!  

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## 0 answers

