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Strand NGS v3.4 - Announcement
Strand Life Sciences announces the release of Strand NGS v3.4.
This release focuses on three aspects:
  • Sample level Quality Control statistics
  • Unique Molecular Identifier enhancements
  • Diverse analysis in Single cell transcriptome studies
New features / Enhancements:
  1. Quality Control
    • An Adapter Content workflow has been added in pre-alignment QC in alignment workflow which enables users to find adapter content in raw sample data. The adapter information can be further used for adapter trimming while running alignment.
    • An Overrepresented Sequences workflow has been added in pre-alignment QC in alignment workflow which enables users to find overrepresented sequence(s) in raw sample data.
    • Find Adapter Content and Find Overrepresented Sequences can be performed in pre-alignment QC in alignment workflow or in QC manager for an analysis experiment. Adapter Content can be inspected at any time in cumulative line-graph format and Overrepresented Sequences can be inspected at any time in tabular format helping the user to get a picture of sample quality before proceeding for analysis.
  2. Unique Molecular Identifier (UMI) enhancements
    • A new UMI protocol, Agilent has been added in alignment workflow where UMI information can be present in a separate file.
    • UMI information and family size information can be exported in SAM or BAM file format as BC tag and YM tag respectively.
    • Support for utilizing the family size information as any custom tag from SAM or BAM file, has been added in all type of analysis experiments.
    • Inspector after Target Region QC workflow for UMI experiment(s) now shows, both family (consensus) and raw reads statistics in respective columns. These columns include: Reads, Avg Coverage, Reads with Padding, Avg Coverage with Padding, and Low Coverage Bases. These statistics will help user to analyze data before and after performing consensus alignment.
  3. Single Cell analysis enhancements
    • Color by feature of t-SNE plot has been enhanced based on gene expression distribution in RNA-Seq, externally quantified (Spreadsheet) RNA-Seq, and Small RNA-Seq experiments.
    • Update Technology Annotations option has been added in right click menu of an experiment to add or modify the technology annotations for the experiment. This will help user to add or modify existing technology annotation post experiment creation and the updated annotations can be further utilized in downstream analysis.
    • Support to create new parameter(s) based on condition clustering results, has been added in Cluster Entities workflow in RNA-Seq, externally quantified (Spreadsheet) RNA-Seq, and Small RNA-Seq experiments. The newly created group(s) can be seen in the Experiment Grouping workflow option.
    • Support to add/update parameter(s) in Experiment Grouping based on condition Principle Component Analysis (PCA) results, has been incorporated in PCA workflow in RNA-Seq, externally quantified (Spreadsheet) RNA-Seq, and Small RNA-Seq experiments.
    • Transformed p-value (-log10p) threshold in volcano plot is now configurable and has been added in right click properties of volcano plot. This will help user to better visualize the transformed p-value of an entity in volcano plot.
  4. Miscellaneous
    • While opening a new analysis experiment, instead of loading all samples only the first sample would be loaded in the Genome Browser read track. This will save time specially in case of analysis experiments with large number of samples.
    • Custom script support in pipeline has been enhanced. Now custom script(s) can be configured during the pipeline configuration time through custom user interface. With this enhancement, there is no need to edit custom script(s) just for changing the configuration.
    • Small RNA quantification can be performed as a background job. This will enable user to work on the tool while running the small RNA quantification job.
    • Support for mate-paired library in MeDIP-Seq experiment has been revoked.
    • Added a checkbox option to ignore mate missing reads in advance parameter section in SNP Detection wizard. This will reduce false positive SNPs in the SNP results.
  5. Server Edition
    • Strand NGS Manager can now be launched from Strand NGS client. Thus eliminating the need for browser with applet support.
Bug fixes:
  1. Split Reads and local realigned reads which were created prior to v3.0 were showing an error in Genome Browser. This has been fixed.
  2. During split alignment, instead of the larger segment being marked as major segment the aligned part was being marked as major. This issue got introduced in v3.0 and could cause some reads to remain unaligned. This issue has now been fixed.
  3. Overlaying line plot was missing from heatmap legend while exporting as report. This has been fixed.
  4. Adding two or more searched experiments to a project was giving an error. This has been fixed.
  5. Split alignment option for non-UMI type experiments in pipeline UI, was functioning inconsistently. This has been fixed.
  6. An unknown error was coming while running pooled analysis for the All Samples interpretation. This has been fixed.
  7. Issue in downloading of interaction DB in server edition has been fixed.
  8. New Project was not getting created from pipeline when there is no active project in the server edition. This has been fixed.
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