RNA-seq alignment in 2 pass mode

Question

[quentin54520]

Hello,

I have RNA seq data from human patient, and I am interested in aberrant transcript analysis (alternative splicing, exon jumping). I would like to know if, it's better to use a 2-pass mode for alignment or assisted by annotation (with a GFF)?

Thanks in advance,
Quentin

[brunobsouzaa]

As you are interested in splice analysis, yes, It's recommended!