format for narrowPeak to show summit position

[Nicolas Bellora]

Dear UCSC Team,

I want to show in a hub track narrow peaks. I followed the instructions from "big format for narrowPeak" discussion and obtained BigBed files. However the summit position is missed in the browser visualization. How can i do to show it?

This is the command line and narrowPeak.as:

TFBS.np is a narrow peak file of macs2, but limiting the score to a max. of 1000.

~/Tools/ucsc/bedToBigBed -as=narrowPeak.as -type=bed6+4 TFBS.np ~/genomes/hg19/hg19.chrom.sizes TFBS.bb

=============
narrowPeak.as
=============

table narrowPeak
"BED6+4 Peaks of signal enrichment based on pooled, normalized (interpreted) data."
(
    string chrom;        "Reference sequence chromosome or scaffold"
    uint   chromStart;   "Start position in chromosome"
    uint   chromEnd;     "End position in chromosome"
    string name;     "Name given to a region (preferably unique). Use . if no name is assigned"
    uint   score;        "Indicates how dark the peak will be displayed in the browser (0-1000) "
    char[1]  strand;     "+ or - or . for unknown"
    float  signalValue;  "Measurement of average enrichment for the region"
    float  pValue;       "Statistical significance of signal value (-log10). Set to -1 if not used."
    float  qValue;       "Statistical significance with multiple-test correction applied (FDR -log10). Set to -1 if not used."
    int   peak;         "Point-source called for this peak; 0-based offset from chromStart. Set to -1 if no point-source called."
)

Thanks,
Nico

[Brian Lee]

Dear Nico,

Thank you for using the UCSC Genome Browser and building narrowPeak bigBed tracks in your hub and your question about the display of the narrowPeak files.

You have helped file a feature request ticket to look into supporting the display of the narrowPeak graphical format when the file is loaded as a bigBed. Currently only with the custom track text format, when the type=narrowPeak is defined, does one see the display of the summit position.

Here is an example text based custom track that can be displayed:

track type=narrowPeak visibility=3 db=hg19 name="nPk" description="ENCODE narrowPeakExample" 

browser position chr1:9356000-9365000

chr1 9356548 9356648 . 0 . 182 5.0945 -1 50

chr1 9358722 9358822 . 0 . 91 4.6052 -1 40

chr1 9361082 9361182 . 0 . 182 9.2103 -1 75

And here is a session that exemplifies the display:

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

Unforunately, since the original coding expected this data to enter the browser as custom text or as MySQL tables, it was not clear that when the data enters as a bigBed file how the display changes and loses the summit. With your mailing list question we have filed a feature request ticket to look into how we cay take an input hub track with bigBeds hosting narrowPeak data and allow the display of the summit position. I have included your email in the future feature request ticket and you will receive a message about any software release regarding this change.

Thank you again for using and suggesting ways to improve 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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