Table Browser Issue

[Sunny Lovell]

Dear team UCSC,

I am currently trying to download a file from the UCSC genome browser(hub_3671779_T2T_Encode_Coverage_SJSA1.H3K4me3 for hs1 in the T2T encode track). I wish to download all of the coverage track data for the Y chromosome; however, the browser sets a limit at 100 000 lines. You do provide a fix to this - filtering the data - but for some reason I get this error when I try to click the button:

• Couldn't set connection database to hub_3671779_T2T_Encode_Coverage_SJSA1
• mySQL error 1049: Unknown database 'hub_3671779_T2T_Encode_Coverage_SJSA1' (profile=<noProfile>, host=localhost, db=hub_3671779_T2T_Encode_Coverage_SJSA1)

Is there any way I can download this information without having to download the entire dataset?

Thanks,

Sunny Lovell

[Matthew Speir]

Hello, Sunny.

Thank you for your question about downloading data from the UCSC Table Browser.

There are three ways you can download data without needing to download the entire file:
1) First, under "Downloads" drop-down in the menu at the top of the page, there is the option to "Download Current Track Data". If the track you're interested in is visible, you should see it listed in the output options. Be sure to enter "chrY" in the search box first to view the entire chromosome. 

2) Second, you can use our command-line utility, bigWigToBedGraph, available here: https://hgdownload.gi.ucsc.edu/downloads.html#utilities_downloads. This command would download just chrY:
bigWigToBedGraph -chrom=chrY https://hgdownload.soe.ucsc.edu/gbdb/hs1/encode/coverage/SJSA1.H3K4me3.chm13v2.0.bw hs1.SJSA1.H3K4me3.chrY.bedGraph

3) Third, we provide a REST API that allows you to download data for a specific track: https://genome.ucsc.edu/goldenPath/help/api.html#getData_examples. However, you're limited to 1,000,000 data points, so you would need to run several queries to get them all. Additionally, the output is in JSON format, so you'd need to do some processing to get it into tsv format. This URL would display the first million bases: https://api.genome.ucsc.edu/getData/track?genome=hs1;track=T2T_Encode_Coverage_SJSA1_H3K4me3;chrom=chrY.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

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Matthew Speir

UCSC Genome Browser, User Support

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