Regarding the extent of expression (fold-change), and considering the subtlety of the very low level radiation treatments, in E. coli three of the four programs gave what we consider exaggerated fold-change results (15 – 178 fold), but one (DNAstar’s DESeq2) gave more realistic fold-changes (1.5–3.5). When RT-qPCR validation comparisons to transcriptome results were carried out, they supported the more conservative DNAstar-D’s expression results. When another model organism’s (nematode) response to these radiation differences was similarly analyzed, DNAstar-D also resulted in the most conservative expression patterns. Therefore, we would propose DESeq2 (“DNAstar-D”) as an appropriate software tool for differential gene expression studies for treatments expected to give subtle transcriptome responses. RNA sequencing (RNA-Seq) has a wide variety of applications in gene expression studies. Since the discovery of RNA’s role as a key intermediate between the genome and the proteome, the quantification of gene expression based on the number of mRNA transcript reads is of great utility in gene expression studies. For older versions, you will need to refer to the information built into your Workbench help to get hold of the relevant manual content.There are several software tools available and still in development for analysis of RNA-seq and for detection of differential expression, but there is no optimal analysis pipeline that can be used for all types of RNA-seq samples. We have online links for earlier version of the CLC Genomics Workbench back to version 6.0 (API 600) and the Main Workbench back to version 6.7.1 (API 671). That is, the above URL should be changed to: The manual provided via this link will be for the current released version of the Workbench.Ĭhange the word "current" to the API version number, which, for the Genomics Workbench 20.0.4, is 2004. current/index.php?manual=Read_mapping.html Here is an example: Let's say you wish to refer to the Read Mapping tool of the Genomics Workbench 20.0.4. If you go directly to the current webpage for the top level section of the manual you are taking to: The easiest way to do this is to go to the link in the current online manual and then edit it accordingly. If you require manual information for an earlier version, you will need to hand-edit the URL with the relevant API number. Note though that the URL you will see at this point is for the current version of the CLC software. Once there, you should see the relevant URL in your browser. To provide direct links to a particular section of a manual, please open the HTML version of the manual and navigate to the relevant section. Manuals for QIAGEN CLC software can be found online at: To reference a particular manual section, the html format of online manual is likely the easiest. The manuals are available in both pdf and html format. For more information, refer to the “ How can I evaluate QIAGEN Workbench and Modules and how long is the evaluation period? ” article at Information related to specific Workbench or Server Analysesīackground information relating to particular analyses can be found in our White Papers and our manual.įor any analysis not covered by a White Paper, please refer to the manual for the product you have been using. The evaluation provides access to all algorithms and is limited to 14 days. Reviewers who want to repeat your analysis can download and use QIAGEN CLC Workbench as it is available for evaluation. The version of the plugin used for the analysis can be found in the history of the output files. For example, when using tools from QIAGEN CLC Microbial Genomics Module version 23.0 within Workbench 23.0.1, use something along the lines ofĬLC Genomics Workbench 23.0.1, CLC Microbial Genomics Module 23.0 () When using tools from QIAGEN CLC Plugins, include the version of the plugin. Hopefully the instructions for authors will indicate the preferences of the particular journal with regards to referencing website in this way. To cite a QIAGEN CLC Workbench or Server product at a general level, please cite our website.įor example, for the Genomics Workbench version 23.0.1, using something along the lines of How can I cite QIAGEN CLC Workbenches and Servers in my paper?Ĭitation guidelines for the QIAGEN CLC WorkbenchesĬiting QIAGEN CLC Workbenches and Server products
0 Comments
Leave a Reply. |
AuthorWrite something about yourself. No need to be fancy, just an overview. ArchivesCategories |