Download all positions where a motif exist from the genome browser
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2.3 years ago
jeni ▴ 60

Hi!

I am interested to know all the positions where a regulatory motif has been described in the genome browser.

I have tried to use the Table browser but there I have to look table by table (using one search with one cell line where the motifs has been validated, another search with another cell line with another motifs, etc). For example: to see CTCF binding sites, I have to perform one query for HM78 cell line, another for K562, etc (and there are different tables fo each one of theese cell lines).

I have also searched in the download part. But there, for some regulatory motifs, there are a lot of different of files to download. For example: all this files are available for Fosl1 binding sites:

wgEncodeHaibTfbsK562Fosl1sc183V0416101PkRep1.sql
wgEncodeHaibTfbsK562Fosl1sc183V0416101PkRep1.txt.gz
wgEncodeHaibTfbsK562Fosl1sc183V0416101PkRep2.sql
wgEncodeHaibTfbsK562Fosl1sc183V0416101PkRep2.txt.gz
wgEncodeHaibTfbsK562Fosl1sc183V0416101RawRep1.sql
wgEncodeHaibTfbsK562Fosl1sc183V0416101RawRep1.txt.gz
wgEncodeHaibTfbsK562Fosl1sc183V0416101RawRep2.sql
wgEncodeHaibTfbsK562Fosl1sc183V0416101RawRep2.txt.gz

and probably I am missing some more entries for this binding site.

So, is there anyway to download all the coordinates, or at least the majority, where a regulatory region, for example, a TFBS is described in the genome browser?

genome • 428 views
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