1
$\begingroup$

I want to retrieve an annotation object (as GRanges) containing different UCSC annotation tracks such as CpG Islands, TSS, TFBS and promoters for hg38 Human reference genome. But "UCSC Genes" was phased out for hg38. What could be the best resource for this ?

Thanks

RT

$\endgroup$
0
$\begingroup$

The UCSC Data Integrator can combine multiple tracks (CpG Islands, TFBS, cCREs, etc.) into one output annotation file, and it works with any assembly you choose. You can select which output fields you want, then download the tab-delimited file.

From there, you can use R, Python, and/or GNU tools such as awk and sed to coerce the data into a format which is useful for your purposes. You can then load it into R as a data frame and use the columns as arguments in the GRanges constructor to create a GRanges object.

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.