Advanced Metadata Topics
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 types.
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:
- Cancer
Indended for: Cancer studies
Configuration:
bih_cancer
Provides: sample specific shortcuts to the latest BAM and VCF files.
- Germline
Indended for: Germline studies
Configuration:
bih_germline
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.
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 ASSAYS
Study Assay File Name a_assay.txt
Comment[SODAR Assay Plugin] samplesheets_assay_generic_raw
SODAR currently supports the following assay plugins:
DNA Sequencing
Generic Raw Data Plugin
Metabolite Profiling / Mass Spectrometry
Microarray
Protein Expression Profiling / Mass Spectrometry
Common links as well as plugin specific links are detailed below.
Common Links
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 filesMiscFiles
: Miscellaneous filesTrackHubs
: Track hubs for UCSC Genome Browser integration (displayed if track hubs have been created)
DNA Sequencing Plugin
Internal name:
samplesheets_assay_dna_sequencing
- Additional assay shortcuts
N/A
- Row-specific links
Each row links to the last material name in the row, not counting “data file” materials.
- Inline links
N/A
- Used with measurement type / technology type
genome sequencing / nucleotide sequencing
exome sequencing / nucleotide sequencing
transcription profiling / nucleotide sequencing
transcriptome profiling / nucleotide sequencing
panel sequencing / nucleotide sequencing
Generic Raw Data Assay Plugin
Internal name:
samplesheets_assay_generic_raw
- Additional assay shortcuts
RawData
: Assay-wide raw data files
- Row-specific links
N/A
- Inline links
Raw data files are linked to
RawData
- Used with measurement type / technology type
N/A (can be used with the
SODAR Assay Plugin
comment override)
Metabolite Profiling / Mass Spectrometry Plugin
Internal name:
samplesheets_assay_meta_ms
- Additional assay shortcuts
RawData
: Assay-wide raw data files
- Row-specific links
N/A
- Inline links
Metabolite assignment files are linked to
MiscFiles
Raw spectral data files are linked to
RawData
Report files are linked to
ResultsReports
- Used with measurement type / technology type
metabolite profiling / mass spectrometry
Microarray Plugin
Internal name:
samplesheets_assay_microarray
- Additional assay shortcuts
N/A
- Row-specific links
Rows with hybridization assay name and scan name are linked under
RawData/{hybridization assay name}/{scan name}/
.
- Inline links
Inline file names are linked to row-specific hybridization assay name and scan name paths.
- Used with measurement type / technology type
transcription profiling / microarray
transcription profiling / DNA microarray
transcriptome profiling / microarray
transcriptome profiling / DNA microarray
Protein Expression Profiling / Mass Spectrometry Plugin
Internal name:
samplesheets_assay_pep_ms
- Additional assay shortcuts
RawData
: Assay-wide raw data filesMaxQuantResults
: Assay-wide MaxQuant result files
- Row-specific links
N/A
- Inline links
Files are linked to
RawData
under the assay.
- Used with measurement type / technology type
protein expression profiling / mass spectrometry