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Add track hubs
Track hubs allow for the display of tracks of data alongside the other data in the Ensembl genome browser. This is a very flexible feature and the data can be hosted anywhere.
The following is an annotated example of an RNA-seq alignment track hub on the Heliconius melpomene melpomene Hmel2 assembly available on ensembl.lepbase.org, which you can adapt to suit your data. Trackhubs are not visible by default but can be displayed by using the cog symbol to configure lowest of the region views on the linked page.

Set up the track hub

Add the track data to a publicly accessible location:
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$ ls -sh /path/to/trackhub/data/rnaseq/heliconius_melpomene_melpomene_hmel2/
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total 2.3G
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98M 13F.bw 103M 15A.bw 101M ERR232445.bw 81M ERR232460.bw
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111M 13G.bw 104M 15B.bw 81M ERR232447.bw 163M SRR2076766.bw
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105M 13H.bw 104M 15C.bw 75M ERR232451.bw 129M SRR2076767.bw
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110M 13I.bw 96M 15D.bw 108M ERR232456.bw 211M SRR2076768.bw
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105M 13J.bw 111M 15E.bw 100M ERR232458.bw 212M SRR2076769.bw
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Create a hub.txt file with a description of the data available in the track hub:
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$ nano /path/to/trackhub/rnaseq/hub.txt
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hub LepBase-RNASeq
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shortLabel RNA-Seq Alignments
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longLabel RNA-Seq Alignments for LepBase
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genomesFile genomes.txt
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Create a genomes.txt file with a 2 line entry for each assembly linking the assembly name to the associated track configuration files:
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$ nano /path/to/trackhub/rnaseq/genomes.txt
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genome Hmel2
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trackDb Hmel2/trackDb.txt
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Create a trackDb.txt file for your assembly:
  • the first section creates a superTrack to group all datasets
  • the following sections define three compositeTracks, one for each of the datasets included in the track hub
  • the remaining sections each specify the path to one of the bigwig files hosted on download.lepbase.org and the compositeTrack to which the sample belongs
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$ nano /path/to/trackhub/rnaseq/Hmel2/trackDb.txt
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track RNASeq
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superTrack on
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group RNASeq
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shortLabel RNASeq
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longLabel Heliconius melpomene melpomene tissues
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html doc/RNASeq
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track WingRNASeq
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compositeTrack on
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group WingRNASeq
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shortLabel Wing RNA-Seq
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longLabel Heliconius melpomene melpomene wing tissues
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html doc/WingRNASeq
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track PRJEB1499
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compositeTrack on
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group PRJEB1499
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shortLabel PRJEB1499
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longLabel RNA-seq of adult Heliconius melpomene rosina male and female chemosensory tissues: antennae, labial palps and proboscis, and legs
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html doc/PRJEB1499
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track PRJNA283415
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compositeTrack on
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group PRJNA283415
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shortLabel PRJNA283415
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longLabel Sex-specific transcriptomes of adult head and abdomen from 3 species of Heliconius butterfly
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html doc/PRJNA283415
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track ERR232445
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parent PRJEB1499
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type bigWig
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bigDataUrl http://download.lepbase.org/v4/trackhub/data/rnaseq/heliconius_melpomene_melpomene_hmel2/ERR232445.bw
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shortLabel ERR232445
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longLabel Hmel_503_F_labial_palps_proboscis
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color 204,0,0
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html docs/ERR232445
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visibility full
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...
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track SRR2076766
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parent PRJNA283415
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type bigWig
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bigDataUrl http://download.lepbase.org/v4/trackhub/data/rnaseq/heliconius_melpomene_melpomene_hmel2/SRR2076766.bw
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shortLabel SRR2076766
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longLabel R29_F_mel_ab
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color 204,0,0
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html docs/SRR2076766
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visibility full
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...
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track 13F
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parent WingRNASeq
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type bigWig
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bigDataUrl http://download.lepbase.org/v4/trackhub/data/rnaseq/heliconius_melpomene_melpomene_hmel2/13F.bw
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shortLabel 13F
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longLabel 13F
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color 204,0,0
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html docs/13F
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visibility full
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...
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For each sample, add an html file with a brief description to a docs folder:
  • this will be displayed if a user clicks the information icon while configuring the display in the Ensembl browser to show/hide tracks
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$ nano /path/to/trackhub/rnaseq/Hmel2/docs/ERR232445.html
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Heliconius melpomene transcriptome sample Hmel_503_F_labial_palps_proboscis (SRA accession: <a href="https://www.ncbi.nlm.nih.gov/sra/?term=ERR232445">ERR232445</a>)
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Add the track hub to your Ensembl browser

Add/edit an assembl-specific configuration file in your Ensembl plugin:
  • update the url to point to your own site
  • remember to commit and push the changes when done
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$ nano conf/ini-files/Heliconius_melpomene_melpomene_hmel2.ini
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[ENSEMBL_INTERNAL_TRACKHUB_SOURCES]
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RNASEQ = genomehubs_rnaseq
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[RNASEQ]
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source_name = genomehubs_rnaseq
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url = http://download.lepbase.org/v4/trackhub/rnaseq/hub.txt
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Restart your Ensembl site to add the track hub:
  • adding the trackhub to an assembly requires a restart, but subsequent changes to the data/configuration files will be picked up automatically
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$ docker rm -f genomehubs-ensembl
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$ docker run -d \
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--name genomehubs-ensembl \
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-v ~/genomehubs/v1/ensembl/conf:/ensembl/conf:ro \
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--link genomehubs-mysql \
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-p 8081:8080 \
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genomehubs/easy-mirror:17.03
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$ docker rm -f genomehubs-ensembl
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$ docker run -d \
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--name genomehubs-ensembl \
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-v ~/genomehubs/v1/ensembl/conf:/conf:ro \
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--link genomehubs-mysql \
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-p 8081:8080 \
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genomehubs/easy-mirror:17.06
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Last modified 1yr ago