Hi Swethaa,
In the future, for a different question topic, I would recommend that you open a separate thread on the board. This makes the question easier to search for other users.
For your first post:
The sj files are only majiq-generated SJ files, not other software. Basically, the build will take all specified experiments in the build config file and make a unified splicegraph. When doing this, a large part of the runtime comes from the process of converting the BAM file into a series of splice junction spanning reads. Sometimes, you might want to re run a build and include new experiments. So, instead of requiring you to re-process the BAM files every time, we specify an intermediate format .sj which will be stored in the .sjdirs location(s). This means, when running the builder with --incremental , the program will not re-process bam files when an SJ file was created previously.
For your second post:
Please note I do not have a good handle on what data is available in IGV. I do not know if de-novo patient specific LSVs would be in their database or not. This would probably require more information about your experiment. Can you give an example of an event you see that is not matching with what you expect?
Thanks,
-San