Hi Nikshep,
Please note that re-building splicegraphs by slowly adding samples is a major planned component of an upcoming release of Majiq V3, which specifically allows building a splice graph with some samples, saving
that splice graph, and using it to calculate psi coverage with other
samples. However, it is not yet out.
For majiq V2.x , there is still an option you can try. If you want to modulize over all samples you will need a combined build over all samples, however, processing the BAM files is the most computational and space intensive part of the build. This is why V2 has a switch --incremental ; basically, in addition to "bamdirs" in the config file, you specify "sjdirs" , and run majiq build with the --incremental flag. This will make majiq convert BAM files into the smaller "sj" files, after which you won't need the BAM files anymore. You can process batches of BAMs this way until you've converted all of them to SJ, and then just run the build over all of the sj files at once. I don't know the specifics of your hard drive space limitation to know if this will completely resolve your issue, but It's worth a shot.
(Also, I can recommend some more hacky workarounds for low-disk-space issues outside of majiq if that's a major problem you are running into on your HPC)
Thanks,
-San