How to detect splice isoforms (no ref. genome)

[Muhammad Mu'izzuddin]

Hi all,
I'm working with Iso-Seq data. Just curious if anyone knows how to detect splice isoform (for no ref. genome).


Thanks in advanced for your help

[bowhan]

The following paper has proposed splicing graph to detect splicing isoforms using EST without a reference genome:

Heber, S., Alekseyev, M., Sze, S. H., Tang, H. & Pevzner, P. A. Splicing graphs and EST assembly problem. Bioinformatics 18 Suppl 1, S181-8 (2002).

There are several implementations. @Magdoll at PacBio has recently developed one for Iso-Seq. It is not officially released though.