Using URLs to encode visibility from a custom trackhub

[Brian Yee]

Hi,

I have a question regarding the using of URLs to control the visibility of a subtrack. I have a trackhub loaded (https://yeolab-trackhubs.s3.us-west-2.amazonaws.com/latest-encore-master-hg38/hub.txt), which I want to URLs to selectively display one or more subtracks (this trackhub is quite large, with over 600 entries). I tried following the example, however am unable to figure out what the subtrack name should be (in the example, this is “gtexRnaSignalSRR1311243”):

https://genome.ucsc.edu/FAQ/FAQlink.html

Track hubs' track visibility can also be changed from the URL parameters. The following link specifies the genome database (db=hg19), loads a track hub (hubUrl=http.../hub.txt), hides all tracks (hideTracks=1), hides the subtrack kids of a particular track (gtexRnaSignalMaleYoung_hideKids=1), sets a specific subtrack to be displayed (gtexRnaSignalSRR1311243=full), and ignores user settings (ignoreCookie=1).

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&hubUrl=http://hgdownload.soe.ucsc.edu/hubs/gtex/hub.txt&hideTracks=1&gtexRnaSignalMaleYoung_hideKids=1&gtexRnaSignalMaleYoung=full&gtexRnaSignalSRR1311243=full&ignoreCookie=1

I tried looking this up via https://genome.ucsc.edu/cgi-bin/cartDump, but was unable to use any of the parameters to show a single subtrack (is there a way to determine subtrack names programmatically)? Could you help me determine what my URL should look like, if I wanted to display the following subtracks from the above trackhub? The following URL does not appear to show anything:

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr22:50434176-50434272&hubUrl=https://yeolab-trackhubs.s3.us-west-2.amazonaws.com/latest-encore-master-hg38/hub.txt&4001_CLIP1_rep1.vs.bb=full&hgt.reset=1&ignoreCookie=1

• 4001_CLIP1_rep1.vs.bb (https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=1545660099_RO7OkmoW02nQ319Kisk0Llh8SK9s&c=chr15&g=hub_2956531_4001_CLIP1_rep1_vs_bb)
• encode4_batch2.4001_CLIP1_CLIP (https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=1545660099_RO7OkmoW02nQ319Kisk0Llh8SK9s&c=chr15&g=hub_2956531_encode4_batch2_4001_CLIP1_CLIP)
• encode4_batch2.4001_CLIP1_INPUT (https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=1545660099_RO7OkmoW02nQ319Kisk0Llh8SK9s&c=chr15&g=hub_2956531_encode4_batch2_4001_CLIP1_INPUT)
• encode4_batch2.4001_CLIP2_CLIP (https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=1545660099_RO7OkmoW02nQ319Kisk0Llh8SK9s&c=chr15&g=hub_2956531_encode4_batch2_4001_CLIP2_CLIP)
• encode4_batch2.4001_CLIP2_INPUT (https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=1545660099_RO7OkmoW02nQ319Kisk0Llh8SK9s&c=chr15&g=hub_2956531_encode4_batch2_4001_CLIP2_INPUT)

Additionally, I tried the following URL patterns to no avail:

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr22:50434176-50434272&hubUrl=https://yeolab-trackhubs.s3.us-west-2.amazonaws.com/latest-encore-master-hg38/hub.txt&ignoreCookie=1&hgt.reset=1&4001_CLIP1_rep1.vs.bb=full # shows genome browser and default tracks, but not 4001_CLIP1_rep1.vs.bb

 

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr22:50434176-50434272&hubUrl=https://yeolab-trackhubs.s3.us-west-2.amazonaws.com/latest-encore-master-hg38/hub.txt&ignoreCookie=1&hgt.reset=1&4001_CLIP1_rep1.vs.bb=full&latest-encore-master-hg38=hide  # sshows genome browser default tracks but not selected track

 

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr22:50434176-50434272&hubUrl=https://yeolab-trackhubs.s3.us-west-2.amazonaws.com/latest-encore-master-hg38/hub.txt&ignoreCookie=1&hgt.reset=1&4001_CLIP1_rep1.vs.bb=full&latest-encore-master-hg38=hide&latest-encore-master-hg38_sel=1  # shows genome browser default tracks but not selected track

 

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr22:50434176-50434272&hubUrl=https://yeolab-trackhubs.s3.us-west-2.amazonaws.com/latest-encore-master-hg38/hub.txt&ignoreCookie=1&hgt.reset=1&4001_CLIP1_rep1.vs.bb=full&latest-encore-master-hg38=hide&hub_2956531_latest-encore-master-hg38_sel=1  # shows genome browser default tracks but not selected track

 

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr22:50434176-50434272&hubUrl=https://yeolab-trackhubs.s3.us-west-2.amazonaws.com/latest-encore-master-hg38/hub.txt&ignoreCookie=1&hgt.reset=1&4001_CLIP1_rep1.vs.bb=full&latest-encore-master-hg38=hide&latest-encore-master-hg38=full  # shows genome browser default tracks but not selected track

 

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr22:50434176-50434272&hubUrl=https://yeolab-trackhubs.s3.us-west-2.amazonaws.com/latest-encore-master-hg38/hub.txt&ignoreCookie=1&hgt.reset=1&4001_CLIP1_rep1.vs.bb=full&hub_2956531_latest-encore-master-hg38=full  # shows genome browser default tracks but not selected track

 

https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr22:50434176-50434272&hubUrl=https://yeolab-trackhubs.s3.us-west-2.amazonaws.com/latest-encore-master-hg38/hub.txt&ignoreCookie=1&hub_2956531_latest-encore-master-hg38=full&hub_2956531_latest-encore-master-hg38_hideKids=1&4001_CLIP1_rep1.vs.bb=full  # shows genome browser default tracks but not selected track

 

Thanks in advance!!

Brian Yee

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Brian Yee

Bioinformatician

Yeo Lab Bioinformatics / SCRM Rm 3115
2880 Torrey Pines Scenic Drive, La Jolla, CA 92037
(858) 534-9322