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,
1 answer
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
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