1. The custom track data may be compressed by any of the following programs: gzip (.gz), compress (.Z), or bzip2 (.bz2). But not for bigwig and bam.
2. In a track hub Db configuration file, up to 9 subgroup types can be defined for a composite, such as:
subGroup1 <gTag1> <gTitle1> <mTag1a=mTitle1a> [mTag1b=mTitle1b…]
subGroup2 <gTag2> <gTitle2> <mTag2a=mTitle2a> [mTag2b= mTitle2b…]
...
subGroup9 <gTag9> <gTitle9> <mTag9a=mTitle9a> [mTag9b= mTitle9b…]
subGroup2 <gTag2> <gTitle2> <mTag2a=mTitle2a> [mTag2b= mTitle2b…]
...
subGroup9 <gTag9> <gTitle9> <mTag9a=mTitle9a> [mTag9b= mTitle9b…]
But these is no such limitation (I guess so, not test yet) for the tag/title pairs in each subGroup. For example, ENCODE data trackDb put all TFs in one subGroup:
http://ftp.ebi.ac.uk/pub/databases/ensembl/encode/integration_data_jan2011/hg19/trackDb.txt
One question: How to share tracks but secure the data files in the track hub?
The current directory hierarchy for a hub is like:
myHub/ - directory containing track hub files
hub.txt - a short description of hub properties
genomes.txt - list of genome assemblies included in the hub data
hg19/ - directory of data for the hg19 (GRCh37) human assembly
trackDb.txt - display properties for tracks in this directory
dnase.html - description text for a DNase track
dnaseLiver.bigWig - wiggle plot of DNase in liver
dnaseLiver.bigBed - regions of active DNase
dnaseLung.bigWig - wiggle plot of DNase in lung
dnaseLung.bigWig - regions of active DNase
...
rnaSeq.html - description text for an RNAseq track
rnaSeqLiver.bigWig - wiggle plot of RNAseq data in liver
rnaSeqLiver.bigBed - intron/exon lists for liver
rnaSeqLung.bigWig - wiggle plot of RNAseq data in lung
rnaSeqLung.bigBed - intron/exon lists for lung
hg18/ - directory of data for the hg18 (Build 36) human assembly
trackDb.txt - display properties for tracks in this directory
dnase.html - description text for a DNase track
dnaseLiver.bigWig - wiggle plot of DNase data in liver
dnaseLiver.bigBed - regions of active DNase
dnaseLung.bigWig - wiggle plot of DNase data in lung
dnaseLung.bigWig - regions of active DNase
...
rnaSeq.html - description text for an RNAseq track
rnaSeqLiver.bigWig - wiggle plot of RNAseq data in liver
rnaSeqLiver.bigBed - intron/exon lists for liver
rnaSeqLung.bigWig - wiggle plot of RNAseq data in lung
rnaSeqLung.bigBed - intron/exon lists for lung
The UCSC webpage also indicates that "unlisted hubs are in no way secure." But this is definitely a unsolved problem. Maybe the only solution is to set up your own local mirror?
I see no point in securing original files of shared tracks. In my lab, we have established our own hub to work conveniently with genomic data, but we don't upload track descriptions until the paper on the data is published. Without descriptions, no one except my colleagues and me may understand what the shared tracks mean.
ReplyDeleteThe genome browser at the University of California Santa Cruz (UCSC) is a popular web based tools for rapidly displaying the requested portion of a genome at any scale.
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