Advanced metadata topics are detailed in this document. These are intended for
e.g. advanced users who manually prepare their own sample sheets for specific
Study iRODS Data Linking
The sample sheet view of the SODAR UI display shortcuts to relevant iRODS files
and IGV integration.
These are displayed on the right hand side column of the study table. The
types of shortcuts displayed depend on the study plugin.
The study plugin selected by SODAR in turn depends on the
study configuration. The configuration usually originates from the template
used to create the sample sheet. SODAR reads this configuration from the
investigation TSV file in a comment labeled
Created with Configuration.
SODAR currently supports the following study configurations:
Indended for: Cancer studies
Provides: sample specific shortcuts to the latest BAM and VCF files.
Indended for: Germline studies
Provides: pedigree specific shortcuts to the latest BAM and VCF files.
If the configuration is not specified or is not known to SODAR, the shortcut
column will not be visible.
Study plugins will search for the “latest” BAM and VCF files for shortcuts and
IGV session generation. This is determined by file name: in case of multiple
files, the last file sorted by file name is returned. Hence to ensure the most
recent file is returned, it is recommended to use dates in the file names.
Placement of files in subcollections under the row-specific collection does not
affect study shortcuts or IGV session inclusion. This also means files can be
freely organized within desired subcollections.
If there is need to omit BAM or VCF files with certain file name patterns from
shortcuts and IGV sessions, file name suffixes can be defined in the
project update view. Administrators can also define
site-wide file suffixes to omit via Django settings
Assay iRODS Data Linking
Similar to study data linking, SODAR also displays iRODS links specific to
assays according to an assay plugin. The selected plugin affects the
following types of iRODS links:
Assay shortcuts card above each assay table
Row-specific links in the right hand column of each row
Inline links which are file names stored in the table itself, under e.g.
“data file” materials.
The assay plugin to be used is determined based on a combination of the
measurement type and technology type attributes of each assay.
If SODAR doesn’t recognize the measurement type and technology combination, no
plugin will be applied. In this case the row-specific links will point to the
root collection of the assay.
Alternatively, it is possible to explicitly declare what plugin should be used
by adding a
SODAR Assay Plugin comment within the
STUDY ASSAYS section
of the ISA-Tab investigation file. As the value for each assay in which you want
to override the plugin, the full internal plugin name (e.g.
samplesheets_assay_generic_raw) should be used. If both the explicit
declaration and measurement/technology type are present, the former will
override the latter. Example:
Study Assay File Name a_assay.txt
Comment[SODAR Assay Plugin] samplesheets_assay_generic_raw
SODAR currently supports the following assay plugins:
Generic Raw Data Plugin
Metabolite Profiling / Mass Spectrometry
Protein Expression Profiling / Mass Cytometry
Protein Expression Profiling / Mass Spectrometry
Common links as well as plugin specific links are detailed below.
Links to the following iRODS collections are provided for all assay
configurations in the assay shortcuts card:
ResultsReports: Collection for assay specific result and report files
MiscFiles: Miscellaneous files
TrackHubs: Track hubs for UCSC Genome Browser integration (displayed if
track hubs have been created)
Generic Raw Data Assay Plugin
Protein Expression Profiling / Mass Spectrometry Plugin
Protein Expression Profiling / Mass Cytometry Plugin