Reusing splicegraph generated by build across multiple samples

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Nikshep Grampurohit be21b025

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Aug 14, 2024, 2:28:09 AMAug 14
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Hi,

I'm currently analysing a large number of samples and my cluster does not have the capacity to process them all at the same time. I am quantifying them in batches by uploading the required files and then deleting them once done. I built my splicegraph using the initial 11 bam files all from one particular group. Further I want to process the other files from different groups. Can I use the same splicegraph as I eventually want to use voila modulize to generate a single folder with psi from all samples? Or will I have to rebuild the splicegraph using the new bam files everytime and figure out a way to merge results later?

Thank you
Nikshep

San Jewell

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Aug 14, 2024, 3:58:12 PMAug 14
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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

Nikshep Grampurohit be21b025

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Aug 17, 2024, 10:31:43 AMAug 17
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Hi San,

Thank you for your prompt response. I was able to build the new splicegraph using the .sj files and it solved my problem.

Would love to your hear your workarounds for low-disk space. 

Thank you
Nikshep

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