Open hkarakurt8742 opened 2 years ago
Hi! thanks for your post and I'm sorry for the delay
We don't have a preference. By default we use STAR and you can check parameters in our publication (https://academic.oup.com/bioinformatics/article-abstract/37/17/2609/6156815?redirectedFrom=fulltext)
This paper can help you as well: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5792058/
And, please, can you post again your issue here so we can open the discussion for more people?
https://github.com/chernolab/ASpli/issues
I will anwer also here :)
Thanks a lot!
Hello everyone, Thank you developing ASPli. I want to use it on some RNA-Seq data but as I guess, the alignment step is crucial in this case. My options are STAR and Hisat2. As I know they are both splice-aware aligners.
Does using splice site annotation for indexing with STAR and Hisat2 affects the results as well? Or indexing with default parameters is okay to use in ASPli?