files of wgEncodeRegTfbsClustered

[yueli8]

Hello,

Thanks so much of this package!

I tried to use Goldmine in R.

Error: Could not open table data URLs (http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/wgEncodeRegTfbsClustered.txt.gz and http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/wgEncodeRegTfbsClustered.sql). Is the table name correct?

Actually, these two files are not in UCSC genome browser. Where I can find these two files?

Thanks in advance for any help!

Best Regards!

Yue

[jeffbhasin]

Hello Yue,
The TFBS supertrack is available under that table name for hg19. In the case of hg38, the TFBS supertrack I do not believe exists (there is only the DNase HSS supertrack). This is because UCSC never created it for this genome build. I would not specify this table when running getFeatures() since it does not exist so there is no data to download. There is however the DNase supertrack (name for hg38 is "wgEncodeRegDnaseClustered"). If there is a specific TFBS of interest and you have a BED file of peaks from some other source, you can always read these in and use them with Goldmine by adding a data.table with the coordinates to the "features" list provided to the goldmine() function.

Jeff