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Performance on WGS and custom coverage plots

asked 2013-06-28 10:25:46 -0700

Michael Rusch gravatar image

Just started kicking the tires, and tried to load a WGS BAM. The cvg and pileup panels initially show "Data is unavailable at this zoom level until background computation is complete." After waiting several minutes, I could see the faintest sliver of green on the progress bar, suggesting that this will be a multi-hour-long process.

We have already generated wiggle plots (in bigwig format) for these BAMs, it would be really nice if we could load the existing plots instead of waiting for new ones. We also generate some custom bigwigs that we would like to be able to load.

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answered 2013-07-02 08:56:03 -0700

Hi Michael,

For whole genome files the first pass when GenomeBrowse is computing index and coverage files can take some time. However, once those files have been generated then you should be able to easily navigate the plot, zoom in and out, or jump to new locations quickly and easily. If you have several WGS BAM files we recommend loading them separately and letting the index and coverage finish computing before loading the next BAM.

Wiggle file support is on our roadmap for GenomeBrowse. We are currently in the process of integrating GenomeBrowse into our analysis software SVS7 and until that has been complete we will not be adding new features to the stand-alone version of GenomeBrowse.

Your feedback is greatly appreciated please let us know if you have any further questions or comments.

Thanks, Jami...

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Asked: 2013-06-28 10:25:46 -0700

Seen: 987 times

Last updated: Jul 02 '13