Software/packages for analyzing differential isoforms from RNA-seq data?

Question

[Kai_Qi]

Hi All:

I am trying to analyze the RNA-seq data created from antibody immunoprecipitated transcripts at nucleus and cytosol. I can use differential gene expression to analyze the different genes but I guess there should be more differences at isoform level since it is a RNA binding protein so it may regulate splicing. I know some software can do splicing analysis like rMATs etc. However, I have to emphasize that I need to get more information at isoform level. I have 1 replicate for IgG at Nucleus and Cytosol fraction.

I am wondering can anyone recommend easy to follow softwares/packages for me to give it a try: currently I use STAR to do alignment and edgeR/lima for differential expression.

Thanks in advance,

Answer 1

[Antonio R. Franco]

Answering a little late

There are many packages available for studying RNA-Seq considering isoforms

• The R package fishpond which uses Swish for inference analysis of isoforms
• The R package EBSeq
• Cuffdiff 2 included in the "old" tuxedo pipeline
• The IsoDE app
• And the Shiny R package Sleuth