Question: reference genome for TFBS
0
gravatar for mariameldova
2.2 years ago by
mariameldova0 wrote:

Hi, I'm looking for an updated TFBS database for hg19 but unfortunately, after the latest release of ensembl regulation, they have not been updated the hg19 version (ftp://ftp.ensembl.org/pub/grch37/update/regulation/homo_sapiens/). How can I use the 85th release?

Thanks!

hg19 tfbs ensembl • 519 views
ADD COMMENTlink written 2.2 years ago by mariameldova0
1

Have you considered working with track hubs from major epigenomics consortia? Look at this tutorial from Blueprint (although I think they have data from histone modifications and DNA methylation, no TFBS).

From the GRCh37 website FTP download doc, it seems to suggest that the Ensembl Regulation data would be updated every now and again. Perhaps it's worth sending the Ensembl helpdesk a message so that they can comment?

The other thing that may be worth looking at is to get the latest data with the GRCh38 coordinates and converting it to GRCh37 (=hg19)..

ADD REPLYlink written 2.2 years ago by Denise - Open Targets4.7k

Thank you for your reply! I considered converting the coordinates but would it be reliable for TFBS? I think since sites ranges from 8-10 to 16-25 bp, it would be more reliable to use motif features to annotate the sites. I contacted with the helpdesk already and am waiting for the reply!

ADD REPLYlink written 2.2 years ago by mariameldova0
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