Tracks can be submitted for assemblies that are already hosted in a GenomeHub. To submit tracks alongside a new assembly, please start with the guide to Submit an Assembly then follow the guidelines below.

Track types

In principle any data that can be mapped to an assembly can be displayed as a track, however adding new types involves a small amount of additional configuration so at present only a limited set of track types have been configured. If you wish to submit other track types, please discuss this with the GenomeHub curator and pick a comparable title for the new track type. Currently accepted types are:

  • RNAseq
  • CHIPseq
  • ATACseq

Data file format

For each track, please supply the data mapped to an existing (or newly submitted) assembly as a bigWig format file. The name of each file will become the display name for the track so please ensure the filenames are short but informative, and use only letters and numbers followed by the .bw file extension.

If submitting bigWig files for more than one track type and/or assembly, please collate the files into a single directory for each track type/assembly combination. Please include track metadata before. Name the directory to match the assembly name and track type, e.g. for RNAseq data aligned to the Heliconius melpomene melpomene Hmel2 assembly the directory name should be Hmel2_RNAseq.

Track metadata

For each track type/assembly combination, please include a single trackDb.txt file in the same directory as the bigWig files. Further information on the metadata format can be found in the TrackHub documentation. The template below uses Heliconius melpomene melpomene RNAseq as an example. Lines beginning with # are comments and should be omitted from your submitted file:

###############################################################
# Top level block defines the track type and species/subspecies 
# Replace all instances of "RNAseq" for alternative track types

track RNASeq
superTrack on
group RNASeq
shortLabel RNASeq
longLabel Heliconius melpomene melpomene tissues

###############################################################
# Tracks should be grouped by study
# For publicly registered data, this should be an INSDC study accession.

track PRJEB1499
compositeTrack on
group PRJEB1499
shortLabel PRJEB1499
longLabel RNA-seq of adult Heliconius melpomene rosina male and female chemosensory tissues: antennae, labial palps and proboscis, and legs

# If you do not have an INSDC-registered accession, please consider registering your study.
# If this is not possible, choose an short, informative name instead


###############################################################
# The remainder of the file should contain one block per track
# As above, naming tracks after INSDC-registered run accessions is preferable
# The "parent" value must match one of the track groups defined above

track ERR232445
parent PRJEB1499
type bigWig
shortLabel ERR232445
longLabel Hmel_503_F_labial_palps_proboscis
html docs/ERR232445
visibility full

track ERR232447
parent PRJEB1499
type bigWig
shortLabel ERR232447
longLabel Hmel_500_M_labial_palps_proboscis
html docs/ERR232447
visibility full

For each track, please also include a basic HTML format file in a docs subdirectory alongside the trackDb.txt file. This file should contain a brief description and a link to and public accessions. It is included in a template file so while html markup is allowed, no headers, etc are required. e.g. for the track ERR232445, a docs/ERR232445.html file would look like:

Heliconius melpomene transcriptome sample Hmel_503_F_labial_palps_proboscis (SRA accession: <a href="https://www.ebi.ac.uk/ena/data/view/ERR232445">ERR232445</a>)

Directory structure

The final directory structure using the examples above would be:

Hmel2_RNAseq
  - docs
    - ERR232445.html
    - ERR232447.html
  - ERR232445.bw
  - ERR232447.bw
  - trackDb.txt

The directory should be compressed prior to submission.