required STAR alignment quality

[Alex PG]

Hi all,

I was wondering if you have any recommendations regarding STAR alignment quality metrics, particularly for the number of input reads, uniquely mapped reads, and reads mapped to multiple loci, in order to achieve the best possible quality for downstream analysis?

Thank you very much for your time, as always.

All the best,
Alex

[Benjamin Wales-McGrath]

Hi Alex,

I would say generally a unique mapping percent of >80% or at minimum 70% is, generally speaking, best for STAR. But we haven't evaluated how these quality metrics affect downstream MAJIQ results.

Best regards,

Benjamin

[Alex PG]

Hi Benjamin, 

Thank you for your helpful answer! It is very helpful, I have found this preprint 

https://www.biorxiv.org/content/10.1101/2024.07.11.603071v1.full

which addresses it, in case you find it interesting.

All the best,

Alex