How to find all of the new RNA splices from bulk RNA-seq data?

Question

[Dan]

Hello,

I found an oncogenic mutation can disturb RNA transcription and maturation, which induces many new RNA splices. Currently, I only have bulk RNA-seq data from several tumor samples with/without this mutation, how can I find all of the new RNA splices from bulk RNA-seq data? Thanks a lot.

[dthorbur]

In addition to what Matthias Zepper wrote, if you have long reads (i.e., PacBio or Nanopore direct-RNA or cDNA) you can also use specific tools that utilise full transcripts like IsoQuant, FLAIR, or ESPRESSO for cis-splicing. They are all reference transcriptome guided approaches.

If you want trans-splicing events, then maybe tools like STAR-SEQR and SLIDR-SLOPPR are appropriate.

[Matthias Zepper]

For a starter, look at the manuals of StringTie or Trinity, depending on if you prefer a reference-guided or de-novo approach. In addition, nf-cores rna-splice pipeline might be useable, although not yet formally released?