New content, new projects, External Scripts improvements and more!
Content updates
Recently-added Lands in OncoLand
OncoLand has added several new Lands over recent releases, be sure to check them out! If you do not see these Lands in your OncoLand collection, please contact your QIAGEN OmicSoft Server administrator to add the Lands to your server.
- BeatAML_B37/B38: In-depth investigation of the various genetic classes of AML that have recently been discovered, with expression and mutation data, as well as ex-vivo drug sensitivity data that can be added as measurements.
- CCLE_DepMap_Preview_B37/B38: All the data in CCLE Lands, with additional gene dependency measurements from CRISPR and RNAi knockdown experiments, as well as new visualizations to correlate these data.
- OncoMouse_B38: Curated oncology studies in mouse model.
Body Maps
GTEx_B37 has 8711 new RNA-seq samples, and 16,964 total RNA-seq samples. GTEx_B38 is scheduled to be updated to GTEx V8 with 2020R2.
Figure 1: Sample distribution of GTEx samples across tissues, colored by whether they were added in the latest release.
New projects in OncoLand 2020R1
Figure 2: New projects in OncoGEO and OncoMouse.
- OncoGEO_B37: 117 new projects, 8236 new samples and 1777 new comparisons
- This release is focused on breast, ovarian, bladder and prostate cancers. New comparisons explore treatment responsiveness, mutation status and more!
- OncoMouse_B38: 33 new projects, 545 new samples and 192 new comparisons
- Hematology_B37: 5 new projects
New projects in DiseaseLand 2020R1
Figure 3: New projects in Human, Mouse, and Rat Disease.
- HumanDisease_B37: 111 new projects, 6724 new samples and 3849 new comparisons
HumanDisease project highlights:
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- A new developmental map of 7 organs from 4 weeks post-conception to adulthood (E-MTAB-6814)
- Inflammatory disease: Effect of stimuli of blood samples from systemic juvenile idiopathic arthritis (GSE103500)
- RatDisease_B6: 14 new projects, over 6112 new samples and 3102 new comparisons
RatDisease project highlights:
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- A new developmental map of 7 organs (E-MTAB-6811)
- Compound profiling in Rat tissues: GSE57822
- MouseDisease_B38: 79 new projects, 2437 new samples and 1102 new comparisons
MouseHumanDisease project highlights:
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- A new developmental map of 7 organs (E-MTAB-6798)
Software updates
Array Suite is now QIAGEN OmicSoft Suite
This is purely a name change to reflect the wide variety of Omics data supported by QIAGEN OmicSoft.
OmicSoft Studio=Array Studio. OmicSoft Server=Array Server. OmicSoft Viewer=Array Viewer.<
Figure 4. New name change of Array Studio as OmicSoft Studio, as part of OmicSoft Suite.
Improved External Scripts with support for Docker technology and cloud analysis
OmicSoft Suite now supports External Scripts on AWS Cloud and can run analyses on Docker images. See some examples here.
These new capabilities substantially expand the options for OmicSoft Suite as an ‘omics data and analysis hub, allowing advanced users who would like to run third-party bioinformatics tools to do so from OmicSoft Suite, and even build pipelines to analyze data and import into OmicSoft projects. Talk with your account manager to learn more about some of the possibilities.
Updates to other OmicSoft Suite functions
Now you can download FASTQ files up to 100GB from the Short Read Archive. Previously, downloading FASTQ data from the NCBI Short Read Archive (SRA) database supported files only up to 20 GB.
The “Single Cell Quantification” function now supports antisense strand reads (commonly generated from 5′ chemistry) in addition to sense strand reads (3′ chemistry), increasing the flexibility to support new workflows.
Figure 5. Example of report for Single Cell Counts.
In “Map RNA-seq reads to genome“, there is a new option to pair input files in the order they were submitted, instead of pre-sorting the files by name. This is useful in exceptional situations, such as when data for the same sample are stored across multiple files in multiple directories, and the file names are identical between directories.
Figure 6. View of how to select to pair input files in the order they were submitted in the “Map RNA-seq Reads to Genome” function.
For example, if your data were run across multiple lanes, and the output files for Read1 are saved as “Batch2_1_S1_L001_R1_001.fastq.gz” in multiple directories (each directory holding data from one lane), you can ensure proper file pairing by specifying the order with “Add List” or during sample registration, and by selecting “pair files in order” when specifying alignment options.
Figure 7. In this example, “Pair Files In Order” will take all the files for Sample201 in the listed order, and properly pair those in folders “aRename” and “bRename”.
QIAGEN IPA/OmicSoft User Group Meetings
Our recent virtual QIAGEN IPA/OmicSoft User Group Meetings that took place in April and May were both a great success. We hope you were able to join us! Review the recordings here.
Stay tuned for more QIAGEN IPA/OmicSoft User Group Meetings taking place later this year.
Learn more about the QIAGEN OmicSoft portfolio here.