In this chapter, we demonstrate how to analyze RNA-seq data and generate interpretable results using CLC genomic workbench software and perform the downstream pathway analysis using ingenuity pathway. Core-genome SNPs were detected using an in-house SNP-pipeline based on GATK and. Analysis of RNA Sequencing Data Using CLC Genomics Workbench Methods Mol Biol. Data for a total of 323 forensically relevant ancestry, identity and phenotypic SNPs can be analyzed, and the resulting genotypes, coverage, quality flags and major allele frequencies are easily compared across samples and platforms.ĬLC Genomics Workbench Forensics Platform agnostic workflow Python Single nucleotide polymorphisms. Sequence reads were de novo assembled using CLC Genomic Workbench. To facilitate the straightforward comparison of genotypes generated from both the manufacturer's software and the independent CLC analysis, a Python script was written. CLC Genomics Workbench 23.0.4 is for research purposes only. Using the vcr2 reference transcriptome de novo assembled in this study as a reference, the variant detection tool embedded in CLC Genomics Workbench was. through CLC Genomics Workbench, obtaining two (left. This paper outlines an automated workflow developed in CLC Genomics Workbench that permits accurate, fast and independent analysis of SNP sequence data from either platform. To ensure the robustness of the SNPs detected as differentiated between the left and right. Currently there is no method to either independently confirm the genotypes determined using the manufacturer's software, or to compare genotypes and quality metrics among samples processed using both platforms. Illumina and Thermo Fisher Scientific have developed assays that permit the sequencing of forensically relevant single nucleotide polymorphisms (SNPs), along with software to determine the associated genotypes. Genotype validations revealed that the Unified Genotyper of the Genome Analysis Toolkit and SAMtools performed significantly better than a caller from CLC.
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