I am not bioinformatician but I am comfortable with the applied side of this field using various tools, mainly windows-based. I have .bam files of my RNAseq data. I have been able to get almost all the necessary analysis done. However, I am facing a problem with visualizing the splicing data.. I want to represent the differences between splicing events in all treatments through some visual tool. There are some available but all are linux-based. Can anybody recommend some good software?
Have you tried loading each .bam file as a track into Integrated Genome Viewer, and switching on the option to display splice junctions? Maybe this will help.
http://genes.mit.edu/burgelab/miso/docs/#what-is-miso
MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples. By modeling the generative process by which reads are produced from isoforms in RNA-Seq, the MISO model uses Bayesian inference to compute the probability that a read originated from a particular isoform.
Loads SAM/BAM files but you have to install Samtools as extra pack
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