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Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline.

Kroll KW, Mokaram NE, Pelletier AR, Frankhouser DE, Westphal MS, Stump PA, Stump CL, Bundschuh R, Blachly JS, Yan P - Cancer Inform (2014)

Bottom Line: Combining these three tools into one wrapper provides increased ease of use and provides a much more complete view of sample data quality than any individual tool.Second is the QC database, which displays the resulting metrics in a user-friendly web interface.The structure of the QuaCRS database is designed to enable expansion with additional tools and metrics in the future.

View Article: PubMed Central - PubMed

Affiliation: Department of Internal Medicine, Division of Hematology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.

ABSTRACT
QuaCRS (Quality Control for RNA-Seq) is an integrated, simplified quality control (QC) system for RNA-seq data that allows easy execution of several open-source QC tools, aggregation of their output, and the ability to quickly identify quality issues by performing meta-analyses on QC metrics across large numbers of samples in different studies. It comprises two main sections. First is the QC Pack wrapper, which executes three QC tools: FastQC, RNA-SeQC, and selected functions from RSeQC. Combining these three tools into one wrapper provides increased ease of use and provides a much more complete view of sample data quality than any individual tool. Second is the QC database, which displays the resulting metrics in a user-friendly web interface. It was designed to allow users with less computational experience to easily generate and view QC information for their data, to investigate individual samples and aggregate reports of sample groups, and to sort and search samples based on quality. The structure of the QuaCRS database is designed to enable expansion with additional tools and metrics in the future. The source code for not-for-profit use and a fully functional sample user interface with mock data are available at http://bioserv.mps.ohio-state.edu/QuaCRS/.

No MeSH data available.


Related in: MedlinePlus

Sample View. Columns can be shown or hidden through the “Select Columns” menu. Visible columns can be sorted by clicking the header and reordered with drag and drop. Clicking on a blue sample name will show a sample report for that sample. Clicking the “Aggregate” button will generate an aggregate report for the samples currently selected using the check boxes.
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Related In: Results  -  Collection


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f3-cin-suppl.3-2014-007: Sample View. Columns can be shown or hidden through the “Select Columns” menu. Visible columns can be sorted by clicking the header and reordered with drag and drop. Clicking on a blue sample name will show a sample report for that sample. Clicking the “Aggregate” button will generate an aggregate report for the samples currently selected using the check boxes.

Mentions: QuaCRS is designed with an interactive GUI as the front end. This is a user-friendly feature important to biologists and core personnel with limited computation experience. QuaCRS is also a time-saving tool for computation staff members, as it conveniently packages all the needed tools in one place, thereby simplifying the execution of a routine data analysis step. A fully functional version of the QuaCRS database populated with mock RNA-seq QC data (five samples, two of which are “combined”), its user interface, and a link for downloading the QuaCRS source code is available at http://bioserv.mps.ohio-state.edu/QuaCRS/. Information about how to log in, navigate, and query QC data using the web interface is provided in the “Readme” page on the QuaCRS website. QuaCRS users need prior administrative approval before they can access their intended QC data. This security feature allows a single instance of QuaCRS to host projects owned by unrelated groups while providing controlled access to individuals designated by the data owners. As depicted in Figure 3, the main webpage displays a table view of all samples present in the database and accessible to the current user. This view facilitates examination of a single sample or multiple samples at once and for all or a few QC metrics. Database filtering can be applied via the “Columns” drop-down menu where QC check boxes are grouped into logical categories based on metric types. Checking and unchecking labels will show or hide the columns in the table view. The table can be sorted by clicking on the labels, and columns can be rearranged via drag and drop. This table may also be filtered by keywords using the search box. The selected keyword(s) can be searched across all columns, or in a specific column using a “column:value” format. The current search function works well to locate non-numeric values such as sample or study identifiers. In future versions, users will be able to filter numerical data by providing minimum or maximum values.


Quality Control for RNA-Seq (QuaCRS): An Integrated Quality Control Pipeline.

Kroll KW, Mokaram NE, Pelletier AR, Frankhouser DE, Westphal MS, Stump PA, Stump CL, Bundschuh R, Blachly JS, Yan P - Cancer Inform (2014)

Sample View. Columns can be shown or hidden through the “Select Columns” menu. Visible columns can be sorted by clicking the header and reordered with drag and drop. Clicking on a blue sample name will show a sample report for that sample. Clicking the “Aggregate” button will generate an aggregate report for the samples currently selected using the check boxes.
© Copyright Policy - open-access
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4214596&req=5

f3-cin-suppl.3-2014-007: Sample View. Columns can be shown or hidden through the “Select Columns” menu. Visible columns can be sorted by clicking the header and reordered with drag and drop. Clicking on a blue sample name will show a sample report for that sample. Clicking the “Aggregate” button will generate an aggregate report for the samples currently selected using the check boxes.
Mentions: QuaCRS is designed with an interactive GUI as the front end. This is a user-friendly feature important to biologists and core personnel with limited computation experience. QuaCRS is also a time-saving tool for computation staff members, as it conveniently packages all the needed tools in one place, thereby simplifying the execution of a routine data analysis step. A fully functional version of the QuaCRS database populated with mock RNA-seq QC data (five samples, two of which are “combined”), its user interface, and a link for downloading the QuaCRS source code is available at http://bioserv.mps.ohio-state.edu/QuaCRS/. Information about how to log in, navigate, and query QC data using the web interface is provided in the “Readme” page on the QuaCRS website. QuaCRS users need prior administrative approval before they can access their intended QC data. This security feature allows a single instance of QuaCRS to host projects owned by unrelated groups while providing controlled access to individuals designated by the data owners. As depicted in Figure 3, the main webpage displays a table view of all samples present in the database and accessible to the current user. This view facilitates examination of a single sample or multiple samples at once and for all or a few QC metrics. Database filtering can be applied via the “Columns” drop-down menu where QC check boxes are grouped into logical categories based on metric types. Checking and unchecking labels will show or hide the columns in the table view. The table can be sorted by clicking on the labels, and columns can be rearranged via drag and drop. This table may also be filtered by keywords using the search box. The selected keyword(s) can be searched across all columns, or in a specific column using a “column:value” format. The current search function works well to locate non-numeric values such as sample or study identifiers. In future versions, users will be able to filter numerical data by providing minimum or maximum values.

Bottom Line: Combining these three tools into one wrapper provides increased ease of use and provides a much more complete view of sample data quality than any individual tool.Second is the QC database, which displays the resulting metrics in a user-friendly web interface.The structure of the QuaCRS database is designed to enable expansion with additional tools and metrics in the future.

View Article: PubMed Central - PubMed

Affiliation: Department of Internal Medicine, Division of Hematology, Ohio State University Comprehensive Cancer Center, Columbus, OH, USA.

ABSTRACT
QuaCRS (Quality Control for RNA-Seq) is an integrated, simplified quality control (QC) system for RNA-seq data that allows easy execution of several open-source QC tools, aggregation of their output, and the ability to quickly identify quality issues by performing meta-analyses on QC metrics across large numbers of samples in different studies. It comprises two main sections. First is the QC Pack wrapper, which executes three QC tools: FastQC, RNA-SeQC, and selected functions from RSeQC. Combining these three tools into one wrapper provides increased ease of use and provides a much more complete view of sample data quality than any individual tool. Second is the QC database, which displays the resulting metrics in a user-friendly web interface. It was designed to allow users with less computational experience to easily generate and view QC information for their data, to investigate individual samples and aggregate reports of sample groups, and to sort and search samples based on quality. The structure of the QuaCRS database is designed to enable expansion with additional tools and metrics in the future. The source code for not-for-profit use and a fully functional sample user interface with mock data are available at http://bioserv.mps.ohio-state.edu/QuaCRS/.

No MeSH data available.


Related in: MedlinePlus