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/CRAM and VCF files.

  • Germline

    • Indended for: Germline studies

    • Configuration: bih_germline

    • Provides: pedigree specific shortcuts to the latest BAM/CRAM 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/CRAM 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 under SHEETS_IGV_OMIT_BAM (also affects CRAM files) and SHEETS_IGV_OMIT_VCF.

Assay iRODS Data Linking

Similar to study data linking, SODAR also displays iRODS links in the assay section 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

Similarly, you can override the assay table row link display with the comment SODAR Assay Row Display. Set it to “true” or “false” (or 1/0) to control whether row links should be displayed for this assay. Note that if you set this to true, the assay plugin used for the assay should implement the get_row_path() method.

STUDY ASSAYS
Study Assay File Name   a_assay.txt
Comment[SODAR Assay Row Link Display] false

SODAR currently supports the following assay plugins:

  • DNA Sequencing

  • Generic Assay Plugin

  • Metabolite Profiling / Mass Spectrometry

  • Microarray

  • Protein Expression Profiling / Mass Cytometry

  • Protein Expression Profiling / Mass Spectrometry

  • Raw Data Plugin

General Concepts

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).

Assay plugins can create the following additional links to connect samplesheet metadata to files stored in iRODS:

  1. Additional assay-wide collections and shortcuts (e. g. RawData).

  2. Creating row-specific collections and shortcuts (i. e. RowPath).

  3. Converting cell values within the Samplesheets table into iRODS/WebDAV links (i. e. inline links).

DNA Sequencing Plugin

Plugin for different DNA sequencing configurations.

  • 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.

    • Creates collections in Landing Zones according to this RowPath.

  • 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 Assay Plugin

Generic plugin which can be used with any measurement and technology type configuration. It enables the user to define row-specific and inline links to iRODS collections via comments in the STUDY ASSAYS section of the ISA-Tab investigation file.

  • Internal name: samplesheets_assay_generic

  • Row-specific links

    • Place one or multiple comments starting with SODAR Assay Row Path.

    • Each comment should define one column name.

    • The comments are evaluated in alphabetical order.

    • Values within these columns are used to define the RowPath.

    • For example:
      STUDY ASSAYS
Comment[SODAR Assay Row Path 1]    Pool ID
Comment[SODAR Assay Row Path 2]    Extract Name
    • Resulting row links:

      /sodarZone/projects/xxx/sample_data/study_yyy/assay_zzz/<pool_id>/<extract_name>/

  • Inline links

    • Comments define semicolon-separated lists of columns to be linked to collections.

    • SODAR Assay Link ResultsReports → ResultsReports

    • SODAR Assay Link MiscFiles → MiscFiles

    • SODAR Assay Link Row → RowPath

    • For example:
      STUDY ASSAYS
Comment[SODAR Assay Link Results]    Report File;Derived Data File
Comment[SODAR Assay Link MiscFiles]  Protocol File;Antibody Panel
Comment[SODAR Assay Link Row]        Raw Data File
  • Used with measurement type / technology type

    • N/A (is only used when the SODAR Assay Plugin comment is set)

Metabolite Profiling / Mass Spectrometry Plugin

Plugin for metabolite profiling assays.

  • 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

Plugin for microarray assays.

  • 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

Plugin for protein expression profiling assays with mass spectrometry.

  • Internal name: samplesheets_assay_pep_ms

  • Additional assay shortcuts

    • RawData: Assay-wide raw data files

    • MaxQuantResults: 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

Protein Expression Profiling / Mass Cytometry Plugin

Plugin for protein expression profiling assays with mass cytometry.

  • Internal name: samplesheets_assay_cytof

  • Additional assay shortcuts

    • N/A

  • Row-specific links

    • Rows with an Assay Name set in the mass cytometry process are linked to {Assay Name} to created one collection per measurement run.

  • Inline links

    • Barcode key and Antibody panel process parameter values are linked to MiscFiles

    • Report file process parameter/comment values are linked to {Assay Name}

    • Raw Data Files and Derived Data Files are linked to {Assay Name}

  • Used with measurement type / technology type

    • protein expression profiling / mass cytometry

Raw Data Assay Plugin

Generic plugin for adding a raw data collection to assays not configured with avspecific measurement type and technology type.

  • 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 (is only used when the SODAR Assay Plugin comment is set)

Warning

This plugin is a candidate for deprecation and may be removed in a subsequent release. It is recommended to use the Generic Assay Plugin instead.