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File size limit

asked 2012-10-01 11:29:27 -0600

Saurav Guha gravatar image

What is the size limit for loading DNA-seq/whole genome data?

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answered 2012-10-01 20:28:38 -0600

updated 2012-10-05 12:36:46 -0600

We have designed GenomeBrowse to scale wonderfully to whole genome DNA-seq data, and there are no hard-coded limits on file size or read density or pretty much anything.

What generally becomes the constrained resource in any big-data visualization system is how much data you can hold in RAM to render your plots in full detail.

Even here we have worked to make the worst-case scenario of millions and millions of reads in a small (<10kb) window at least not break GenomeBrowse. Instead, we drop some reads from the pile-up plot while continuing to count them in the coverage plot. You will get a little warning icon on the bottom of your pile-up plot if you do ever get to such a high-density region.

If you experience any failures to handle large files, we would consider it a bug. In such cases we ask for your help if at all possible to share your data securely so we can reproduce and resolve the issue.

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Asked: 2012-10-01 11:29:27 -0600

Seen: 986 times

Last updated: Oct 05 '12