1/13/2024 0 Comments Clc genomics workbench ucsfMessage me if you'd like to see some codes I've used or have any other questions. I would encourage you to seek further support in your research community and start fiddling around with RStudio and these various packages. I feel publishing with these types of R packages are more credible in the literature as well. I don't know where you are at in your career, but learning these tools has made me feel ahead of the game and more trusting of my results. Many others have stood where you're standing, resulting in a lot of blog posts etc. ![]() Although, command line analysis is quite difficult at times to learn and incredibly frustrating, it's not impossible. Therefore, I would advise to use CLC as more of a preliminary analysis tool. I ended up getting clearer results that I trusted and understood better after abandoning CLC and using DESeq and EdgeR (with DESeq being my preferred method). Hi Cristina, I previously used CLC for RNA-Seq analysis and fiddled with lots of parameters, my final output delivered a low number of differentially expressed genes (DEG) that were uninformative. the oligo pair-annealing score." Not very helpful in my view.) the secondary structure score and parameters pertaining to oligo-pairs such as e.g. The algorithm considers both the parameters pertaining to single oligos, such as e.g. (Edit: From the help menu: "CLC Main Workbench employs a proprietary algorithm to rank primer and probe solutions. However, since you are quite free to set a multitude parameters, I guess that the hits are scored mainly based on fitting these as well as the alignment with the homolog sequences. Features for the Genomics Workbench are described below: Analyzing and visualizing Next Generation Sequencing data, incorporates cutting-edge technology and algorithms, while also supporting and integrating with the rest of your typical NGS workflow. I didn't really get any insight into the algorithm that CLC uses to determine primers in the manual. The CLC Genomics Workbench is the client software for the CLC Genomics Server. While checking the software options I saw that most people recommend Primer3 in this context. ![]() However, I didn't use it for TaqMan probes yet. It offers convienient options to design primers from alignments that are able to discriminate between rather homolog sequences. Since I am used to do primer design in the CLC Main Workbench that would obviously be my first choice. ![]() I want to design primers/probes for a TaqMan application.
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