I am new to RNA-SEQ data analyses, I am interested to know if you know any tutorials which specifically describes RNA seq alignments etc in IGV. I am able to load my alignments with ref. But I couldn't find any tutorial which mainly describes each of alignment details in IGV. ( I read through IGV docs, also watched youtube videos).
You might also look at IGB for RNA-seq visualization as well. Biggest difference between IGB and IGV is you can interact with the reads and gene models. For example, you can right-click a gene to run a google or blast search. You can also click-drag over a region to select and count reads, which is nice when you need to get an idea of gene expression levels or check your read counting software results. You can also show or hide reads based on whether they have introns or other attributes, which is sometimes useful. The other big difference is that zooming is very fast in IGB - you can go from chromosome to base pairs in a flash. However, if you need to see how paired end reads are connected, IGB can't do that yet.
Truth in advertising: I am one of the IGB developers :-)
The tutorial uses an example data set from the central data repository for IGB, called IGBQuickLoad. But of course you can open and load your own files.
I would look at the SAM specification. When you hover over a read, you're getting SAM information in that little window that pops up. I think of IGV as a "SAM visualizer".
Is that what your question hinges around (read details)? There's also track visualization and things like that, but that's usually more specific to what a user is wanting to study.
[Update based on your comment]
There are some reserved colors to denote insert size anomalies--specifically, red and blue, as described here. Look under the "Paired End Alignments" section.
In short, a paired-end read shaded gray indicates a concordant alignment (both alignments on the same contig). If a pair is discordantly mapped, the read's mate is shaded based on the contig/chromosome it's mapped to. So if you see two reads shaded pink, it means both their mates are mapped to the same contig/chromosome.
Thanks for your answer. I am basically trying to understand the alignment view. Like some of the exons are colored and some are gray, how to look for alternative splicing etc.
Thanks to all for your responses.