superTranscript for differential gene expression analysis

[clin...@umn.edu]

Hello,

According to the algorithm paper of superTranscript (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1284-1).  SuperTranscript can be used for differential transcript usage. However, I don't whether supertranscript can be used as genes, and do differential gene analysis.  If not, what is the major problem?

Thank you very much.

Chen Lingyun

[Nadia Davidson]

Hi Chen Lingyun,

You can definitely use superTranscripts to do gene-level differential expression analysis too. We don't really discuss this in the superTranscript paper, because we believe it would perform much the same as using the gene-level counts that come directly out of corset, and using just corset involves running less software.

Cheers,

Nadia.