Which alignment method and indexing options are suitable to use in ASPli? - Githubissues

estepi / ASpli

Analysis of alternative splicing using RNAseq

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Which alignment method and indexing options are suitable to use in ASPli? #23

Open hkarakurt8742 opened 2 years ago

hkarakurt8742 commented 2 years ago

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?

estepi commented 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!