TFBS Uniform track

[Katarzyna Wręczycka]

Hi,

Where can I find bigwig files from Uniform track that correspond to files from the website http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeAwgTfbsUniform (files in narrow peak format I found here http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeAwgTfbsUniform/). I can see that most of them are here http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/supplementary/integration_data_jan2011/byDataType/signal/jan2011/bigwig/, but I can't find there all files that correspond to narrowpeak files in the Uniform UCSC track (e.g. I can't find bigwig file for IMR90 CTCF). Is it because these bigwig files are from Jan 2011 Release? If yes, then where can I find bigwig files and bam files used to create Uniform track from higher release?

Best,

Katarzyna Wreczycka

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Katarzyna Wreczycka

PhD student
Bioinformatics Platform
The Berlin Institute for Medical Systems Biology (BIMSB)
Max Delbrück Center (MDC)
Robert-Rössle-Straße 10
House 87, room 1.10
13125 Berlin, Germany
Phone: +49(0)17628595329

Web: http://bioinformatics.mdc-berlin.de

[Brian Lee]

Dear Katarzyna,

Thank you for using the UCSC Genome Browser and your question about the underlying bigWig files that correspond to the TFBS Uniform Track.

Thank you for including the link to the Uniform TFBS Track Track Description page, http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeAwgTfbsUniform , where you find a line sharing the following:

The primary and lab-processed data (along with methods descriptions, credits and references) on which this track is based are available in the following ENCODE tracks: HAIB TFBS, SYDH TFBS, UChicago TFBS, UTA TFBS, UW CTCF Binding. These tracks are accessible from the ENC TF Binding Super-track .

Also on that page you will find information under the Methods section that details how original mapping of the BAM files were used and various forms of quality control and final peak calling was performed.

If you are seeking the uniform bigWigs used to build these tracks, they were not retained in the methods process. However, if you were seeking the original BAM files, and the lab generated bigWigs, you can view those, but they will not be uniformly processed.

You may be more interested in accessing the AWG Hub, also referenced in your email, here is a link to visualize the hub:

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt

If you go to the http://genome.ucsc.edu/ENCODE/downloads.html page, you will find a "Human Genome Build 37 (hg19): ENCODE Analysis Hub at the European Bioinformatics Institute" section that refers to all the files for the Hub.

Navigating the AWG Hub's Uniform TFBS Track titled "ENCODE Transcription Factor ChIP-seq Peaks and Signal based on Uniform processing pipeline" you will find that both "Peaks" and "Signal" tracks are available:

http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=hub_4607_uniformTfbs&hubUrl=http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hub.txt

Here is a session of the hub displayed where both a select number of Signal and Peak files are displayed:

http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=brianlee&hgS_otherUserSessionName=hg19.AWG.Hub.TFBS

Links to these displayed files are featured on the http://genome.ucsc.edu/ENCODE/downloads.html page. You can also go the Table Browser to output only selected regions of these files from the AWG Hub.

You can also view the underlying stanza's that define the hub by navigating the hub's hg19 trackDb.txt page,http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hg19/trackDb.txt, and searching for all lines that have "parent uniformTfbsSignals" and specifically bigDataUrls a file.bw will give you the file locations of the displayed items in the hub. Here is an example curl command to select these:

curl -s http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hg19/trackDb.txt | grep -C 2 "parent uniformTfbsSignal"

As you have noticed there is a difference between the number of files in the AWG Hub and the UCSC TFBS Uniform Track. There is a note on the UCSC TFBS Track Description page titled "Differences from the January 2011 freeze pipeline" to explain the divergence.

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genomics Institute

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