how to choose the best RNAseq protocol for patients sample

Question

[ashkan]

we are designing a project in which we would like to perform the following analysis on the patients data:

1- gene expression
2- alternative analysis
3- mono allelic expression
4- gene fusion

to do so, we have to choose the best protocol for the RNAseq data (considering the mentioned analysis). do you know which protocol (rRNA Depletion / Poly-A Selection) would be the best for our experiment and why?

[Matthias Zepper]

Since this is a bioinformatics forum, I fear that you will find only limited information on wet lab protocols here and that asking at a platform like protocols.io or seqanswers might be more helpful. Reaching out to Clinical Genomics Facilities might also provide you with helpful tips. Generally, a lot of kits (and computational pipelines!) will not be certified for diagnostic use, so your choice is anyway very limited.