What is the size limit for loading DNA-seq/whole genome data?
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.
Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.
Asked: 2012-10-01 11:29:27 -0700
Seen: 64 times
Last updated: Oct 05 '12