New bigNarrowPeak format in v358 for custom tracks and track hubs and enhanced pennantIcon

[Brian Lee]

In v358 we released today support for a new track type bigNarrowPeak and an enhancement to pennantIcon to allow any text display.

For custom tracks there has been a text-based type narrowPeak (http://genome.ucsc.edu/FAQ/FAQformat.html#format12) used often in ENCODE, here is an example version:

track type=narrowPeak visibility=pack db=hg19 name="nPk" description="ENCODE narrowPeak Example"
chr21 33033812 33034920 . 100 . 182 5.0945 -1 50
chr21 33036028 33037136 . 400 . 910 4.6052 -1 40

When this track type was converted into a bigBed, it would not display the peak the same way, even when the correct .as file was specified for each column.

We have now instituted a type bigNarrowPeak, so that any previous bigBed that had been built with the proper narrowPeak .as file will display correctly provided that instead of "type=bigBed" is used, the "type=bigNarrowPeak" is used (or "type bigNarrowPeak" in hubs). Here is an example from the ENCODE 2012 AWG Hub and from the current ENCODE portal loaded as custom tracks:

track type=bigNarrowPeak visibility=full db=hg19 name="nPk" description="AWG ENCODE narrowPeak Example" bigDataUrl=http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipGm12878Pol2AlnRep0_VS_wgEncodeOpenChromChipGm12878InputAln.bb

track type=bigNarrowPeak visibility=full db=hg19 name="nPkENCODE" description="Portal ENCODE narrowPeak Example" bigDataUrl=https://www.encodeproject.org/files/ENCFF859UYN/@@download/ENCFF859UYN.bigBed?proxy=true


The other change to hubs in v358 is new support for pennantIcon to take text and color to help highlight new tracks in hubs, for example with the wording "New" in red.  The below stanza both illustrates the bigNarrowPeak in a hub and the pennantIcon change:

These type will similarly work in a track hub with stanzas such as:

track exampleNewTypeBigNarrowPeak
type bigNarrowPeak
visibility full
shortLabel Peaks
longLabel AWG ENCODE narrowPeak Example as bigNarrowPeak previously defined as type bigBed
bigDataUrl http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/byDataType/peaks/jan2011/spp/optimal/hub/spp.optimal.wgEncodeOpenChromChipGm12878Pol2AlnRep0_VS_wgEncodeOpenChromChipGm12878InputAln.bb
pennantIcon New red

Further documentation about the new bigNarrowPeak type is coming and will be found on the track hub definitions page (http://genome-asia.ucsc.edu/goldenPath/help/trackDb/trackDbHub.html) and a future announcement.