hg19 and hg38 where do the repeat Annotations come from?

[jo-mc]

About Info on the track points to https://jbrowse.org/genomes/hg38/repeats.bb

What is the source of this info?
Do you generate the bb file, and if so where is the code for doing this?

Thanks.

[cmdcolin]

Hi @jo-mc
I actually don't have good provenence on this file, but I think I made it awhile ago.

It was probably generated from UCSC Table Browser, selecting repeats, RepeatMasker, get output as BED
https://genome.ucsc.edu/cgi-bin/hgTables?hgsid=1028457289_xuPfKZcYbYCm3RHzKfngPzDa9lLe&clade=mammal&org=Human&db=hg38&hgta_group=rep&hgta_track=dbSnp153Composite&hgta_table=0&hgta_regionType=genome&position=chrX%3A15%2C560%2C138-15%2C602%2C945&hgta_outputType=bed&hgta_outFileName=

This can then be converted to bigbed with bedToBigBed

I could probably create an updated version of this with a bit more provenance in the "About track" panel

[cmdcolin]

would probably be worth adding the other types of repeat tracks too !