Find & download exact bed file corresponding to UCSC browser track

[afkoeppel]

Hello everyone,

I'm trying to determine the best way to get a BED file (or any file with positional information that I could coerce into a BED file) for a specific track appearing in the UCSC genome browser window.

I've successfully done this sort of thing several times in the past, but this particular file is eluding me.

The particular track I'm looking for is the CTCF ChipSeq peaks for cell line A549. When using the checkbox table on UCSC, the track name:

A549 with DEX_100nM PeakSeq TFBS Peaks of CTCF from HudsonAlpha

...comes up as one of the options when checking the box for which tracks to show in the brower window: https://genome.ucsc.edu/cgi-bin/hgTr...07_uniformTfbs

However, when searching for that track (and the elements of the track in different combinations) on the downloadable ENCODE files page, I get no results. https://genome.ucsc.edu/cgi-bin/hgFi..._Search=search

See attached images.

I also went to ENCODE to see if I could get the file directly from there, and I downloaded the file: wgEncodeAwgTfbsHaibA549Ctcfsc5916Pcr1xDex100nmUniPk.txt.gz

...which appears to correspond to the track I want, but when I load the intervals into the browser, it doesn't seem to match up exactly with any of the tracks. (see Browser_window.png, attached).

Any insights as to how I can get at a bed (or similar) file for this specific track would be much appreciated. I apologize if the answer ends up being easy or obvious, but I've been beating my head against this for awhile now so I figured it was time to ask for some help.

Thanks,

Alex Koeppel

[GW_OK]

Have you tried the UCSC table browser (it's in the tools header)?
It's my preferred method for getting beds from UCSC.
I downloaded a bed file with the track name you gave.

https://genome.ucsc.edu/cgi-bin/hgTa...gsid=365532131

[Thias]

The UCSC table browser is unfortunately limited to a certain number of output regions - 100.000 and can be increased with some tricks. However in some cases this is still too less to allow downloading the whole genomewide track.

I would rather take the approach via GEO Datasets. The study you are interested in is GSE32465. Have a look at the samples there and select the appropriate one - I think GSM803453 is what you are looking for, but doublecheck yourself please.

The broadpeak files are actually bed files with some additional columns.

[afkoeppel]

Thank you both very much. I tried both ways and was able to get the file I needed. I very much appreciate your help with this.