Batch Queries - No output for non-matches

[Letha Sooter]

Hello.  I am running batch queries using the Table Browser by pasting in a list of defined regions.  The output contains data when one of the defined region queries matches that of a gene, but there is no data output when one of the define region queries does not match that of a gene.  This is making it difficult to match my output back to my original list of defined regions.  Is there a way to include regions that don't match a gene in the output?  Or, is it possible to include the defined region input in the final output?

Thank you for your help!

Best,

Sooter

[Daniel Schmelter]

Hello Sooter,

Thank you for using the Genome Browser and for your question about finding data that does not intersect with a particular gene dataset.

The intersection of two datasets can be found with the Table Browser intersection feature. This feature also includes the "... records that have no overlap with GENCODE v29" option as the second from the top button from the intersection page. This will show you items that do not overlap with your selected gene set. Doing two different queries will allow you to find both the intersection and the non-intersection data.

Here are short instructions for doing a NOT intersect. From Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables), begin by selecting your uploaded Custom Track or Track Hub data, making sure the assembly is correct and that the region is set to "genome". Then click the "create" button next to the intersection field. Select a dataset, such as "GENCODE v29 (knownGene)". Select the second from the top radio-button on that page labeled "All User Track records that have no overlap with GENCODE v29". Clicking "submit" and proceeding through the options will give you every one of your items that did not overlap with any gene exons. This result can be considered alongside the regular intersection to show, in two files, which data intersected and which did not.

For a more general explanation of finding genes in a region, you may be interested in the tutorial video (https://www.youtube.com/watch?v=RjB_N1GpT0U). If you would like to combine columns from your dataset and a gene set line-by-line, you may be interested in using the Data Integrator tool (http://genome.ucsc.edu/cgi-bin/hgIntegrator).

I hope this was helpful. If you have any more questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,
Daniel Schmelter
UCSC Genomics Institute

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