Percent DNase I Hypersensitive

[Rosenbaum, David J - (djr1)]

Hello,

First off, thank you for answering all my questions.

Here is another...

I have a list of 2.1 million probe locations and would like to know the percent DNase I hypersensitive. Am I stuck due to the limiting upload of 1000 defined regions in the table browser? or is there another way to determine this percentage?

Thank you,

Dave

[Brian Lee]

Dear David,

Thank you for using the UCSC Genome Browser and your appreciation of our support. It is not readily clear what you may be attempting for your research without examples.

Perhaps you may be submitting through the table browser a selection of defined regions, and then perhaps clicking the "summary/statistics" button against a DNase track to get desired output like "Item bases 2,128,151 (3.95%)"? There may be some technical solutions, depending on an understanding of what you are attempting, however, they may be more challenging to pursue for someone less familiar with computers as you mentioned.

You might be interested in the DNase Clusters track, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeRegDnaseClusteredV2. This track shows DNase hypersensitive areas assayed in a large collection of cell types, aggregated and uniformly processed. In the table browser you can select the "Regulation" group, "DNase Clusters" track, and the "wgEncodeRegDnaseClusteredV2" table, and then click the "describe table schema" button to learn more about this data in BED format.

If you created a custom track of your regions, one approach you can take is to do an intersection of your data with the tables you may be interested in, such as the wgEncodeRegDnaseClusteredV2 table. However, performing an intersection with a custom track with 2.5 million regions using the Table Browser will likely time out. To learn more about creating a custom track please review the User Guide:http://genome.ucsc.edu/goldenPath/help/customTrack.html, I also recommend watching this Table Browser Custom Track tutorial:http://www.openhelix.com/cgi/tutorialInfo.cgi?id=28. Also, read about performing intersections with the Table Browser here:http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html#Intersection

More technical solutions could be to download some tools available from our utilities directory, http://hgdownload.cse.ucsc.edu/admin/exe/, specifically bigWigAverageOverBed. This program will complete an intersection with a bed file and a bigWig file. Depending on what you are attempting to do, you perhaps could also perform MySQL queries on the tables of interest, please read more here:http://genome.ucsc.edu/goldenPath/help/mysql.html

Without a clear picture of what you are attempting it is hard to direct you on the best path. Thank you again for your inquiry and using the UCSC Genome Browser. If you have further questions, please feel free to contact the mailing list again at gen...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genome Bioinformatics Group

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