Subio Platform v1.26.5949 has been released. This update expands RNA-Seq analysis options and output formats for FASTQ files, and introduces support for pausing and resuming processing. It also adds a comparison feature to Enrichment Analysis and a new feature for inspecting intermediate values during normalization. Various improvements have also been made to Venn Diagrams, filtering, data management, and other features.
Here are the main changes since v1.25.5867.
Kallisto Support for RNA-Seq Analysis
In addition to the existing HISAT2 + StringTie pipeline,
Kallisto is now supported for quantifying expression from RNA-Seq FASTQ files.
Expression values can now be saved at both the gene and transcript levels.
The software generates tables for individual samples
as well as combined tables containing expression values from multiple samples.
For details, see How to Process RNA-Seq FASTQ Files .
Pause and Resume Support for FASTQ Processing
RNA-Seq FASTQ import and
FASTQ to VCF
now support safe pausing and stopping,
as well as resuming processing from previously saved results.
Results from previous runs are checked for each sample and processing step,
allowing completed steps to be reused and processing to resume from the appropriate step.
Automatic retries after failures, exclusion of invalid FASTQ files,
and retries with fewer threads or reduced parallelism are also supported.
Comparison Feature Added to Enrichment Analysis
The Enrichment Analysis tool in the Advanced Plug-in now allows
two gene lists to be analyzed under the same conditions,
with the results displayed side by side for comparison.
Users can identify GO terms and pathways shared by both results
and see the percentage of entries in each result list that also appear in the other.
Venn Diagrams can also be used to visualize the overlap between the results.
For details, see How to Use the Enrichment Analysis Tool .
Other New Features and Improvements
| Feature | Changes |
|---|---|
| RNA-Seq Sample Import | Users can now choose between Gene ID and Gene Symbol when importing samples. Count values are imported as Raw Signal, and TPM values as Reserved Signal. The import workflow after analysis completion has also been refined, along with the column order and initial display of Sample Information. |
| Saving and Loading fastp Options |
fastp options can now be saved as named presets and loaded for subsequent processing. These presets are also included in full data backups. |
| Venn Diagram Improvements |
Venn Diagrams now use area-proportional representations for up to three sets. When selected regions are saved as lists, names are automatically assigned based on the selection. The # Overlaps feature has also been improved, allowing all lists in a folder to be added at once and input lists to be removed in a single operation. |
| Filter Tool (Basic Plug-in) |
Filtering by Skewness has been added. Calculated statistics can also be saved to a Measurement List. Histograms now support horizontal and vertical zooming, as well as resetting to the original zoom level. |
| Intermediate Signal |
Users can now pin any step in the Normalize workflow and save the values at that stage as Intermediate Signal. One Intermediate Signal can be saved per Series and viewed in various Views and Datasheets. |
| Merge Platforms |
Merge Platforms now uses a step-by-step wizard for comparing Measurements and selecting columns to merge. |
| gzip-Compressed Files | Support for importing gzip-compressed files has been expanded for Samples, Platforms, Genomes, Measurement Lists, Region Lists, Look Up, and other data types. gzip-compressed output is now also supported for Region Lists. File input fields now indicate supported formats and gzip compatibility. |
| Table and Graph Operations | Select All and Deselect All options have been added for choosing output columns. Buttons have also been added for changing point sizes in Scatter Plots. The Tab key navigation order in search and replace panels has been standardized. |
| Display and Memory Settings | Unnecessary table resizing and redraws when opening or closing selection panels have been reduced. The automatic maximum memory allocation setting has also been revised to reserve more memory for the operating system and other applications, helping Subio Platform run more reliably. |
| Help and Settings | Help links for import procedures, instructions for downloading reference data via HTTPS, and GATK4 configuration labels have been updated. |
Bug Fixes
| Area | Fixes |
|---|---|
| Data Import | Fixed an issue that prevented users from changing the Platform or filtering conditions and retrying after a failed Sample import. Issues with recovering from Look Up import failures and duplicate processing starts have also been fixed. |
| gzip File Import | Fixed an issue where closing a window during file loading preparation could leave the original window unresponsive. |
| Sample Information | Fixed issues where repeated entries in SOFT files could be lost and viewing a cell could unintentionally modify its XML content. Issues with importing RNA-Seq TPM information and attaching Kallisto reports have also been fixed. |
| Column Editing and Undo/Redo | Fixed issues where editing or deleting columns, or performing Undo and Redo operations, could cause columns and their values to become misaligned. |
| Attached Files | Fixed issues with attached file operations and drag-and-drop export. Exporting attached files is now handled as a copy operation. |
| Volcano Plot | Fixed an issue where selections were not updated correctly when threshold values were changed. |
| Summarize | Fixed the summarization of regions with a start coordinate of 0 and improved the handling of invalid and large coordinate values. |
| Regions | Fixed an issue where the Regions tab could disappear even when Region Lists were still present, as well as errors caused by operations performed without a selected list. |
| Annotation Search | Fixed an issue where search conditions were lost when switching Measurement Lists. |
| Adding and Removing Samples | Fixed an issue in Add/Remove Samples where sample checkboxes could become unintentionally unchecked. |
| Display and Help | Fixed unnecessary redrawing when opening or closing plug-in panels and an issue where Import Samples Help could open twice. |
Changes and Important Notes
- Direct import of SAM/BAM and BAR files has been removed. SAM/BAM processing within FASTQ analysis remains available.
- Links to the FASTQ support service scheduled for discontinuation have been removed.
Updating Subio Platform
To update Subio Platform, select "Check for Updates..." from the Help menu, or download and run the appropriate Updater below.
IMPORTANT: Starting with v1.25.5867, the Mac version of Subio Platform supports only Macs with Apple Silicon. Do NOT update on Macs with Intel processors.