Hi all

I am totally new in bioinformatics and I need to analyze some RNAseq data to reconstruct differential expression of exons and isoforms and the specific splicing events. After a lot of (confusing) reading I decided to use BitSeq for the isoform analysis and spliceR for the splicing events (the exon usage recontruction was already done by someone else using DEXSeq).

I am still in doubt whether would be better to use edgeR instead of BitSeq, but reading the manuals I found somehow easier BitSeq and since I'm working with mouse data the "assumption of known model" is satisfied. Does anyone have any suggestion about the which tool would be  better to use and in which situation?

Also I would like to know if it's possible to use the BItSeq (or edgeR) data as input for spliceR, as i think this would be more consistent as compared to run Cufflinks and use that output for spiceR.

I know that spliceR accepts inputs also from other transcripts assembler than Cufflinks but I'm worried that there might be a problem to use BitSeq data as, in contrast with Cufflinks, it uses a transcriptome-based alignment instead of a genome-based alignment.

I would like to obtain the most accurate and consistent data on all the 3 levels of analysis. Any comments/suggestion about this workflow would be highly appreciated.

Thanks!