Number of genes

Hajar

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Nov 30, 2021, 1:12:08 PM11/30/21

to gen...@soe.ucsc.edu

Dear,

Is it possible to get the total number of genes in a region in the UCSC genome browser. I managed to download the list of genes by using the table browser tool, however I also want to get the total number of genes in that specific region.

If there is a way, this would be easier than counting all the genes in the list.

Thank you in advance,

Hajar

Daniel Schmelter

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Nov 30, 2021, 2:29:12 PM11/30/21

to Hajar, UCSC Genome Browser Support

Hello Hajar,

Thanks for contacting the Genome Browser support team with your question about getting the number of genes in a region.

You can count items in a region using the Table Browser's Summary/Statistics button. This option is at the bottom right of the Table Browser page. This button will tell you the number of items in a dataset as well as various item size statistics for the "Region of Interest". Check that you have the correct region because Table Browser defaults to the whole genome. You should also know that any filters applied on the Genome Browser visual display will need to be re-applied in Table Browser.

For example, the default gene set for hg38 is GENCODE V38 and has the default filter of "Basic Only" transcripts displayed. The output will count every item in the dataset within the given region, including items with the Comprehensive tag that aren't normally displayed. If you want to filter to Basic only, you can click filter: "create" and then enter "*basic*" in the tag field. The Summary button output will then show the number of items in the region that passed the filter.

If you have any more questions, please reply-all to gen...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, please reply-all to genom...@soe.ucsc.edu.

All the best,

Daniel Schmelter
UCSC Genome Browser

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Daniel Schmelter

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Nov 30, 2021, 3:18:47 PM11/30/21

to Hajar, UCSC Genome Browser Support

Hello Hajar,

Additionally, if you want one transcript per gene instead of multiple transcripts, the knownCanonical table for the GENCODE V38 track already is filtered to a single transcript per gene. If you select this table, you can avoid using any tag filters. It may be more simple.