2020
DOI: 10.1007/978-1-0716-0223-2_4
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Analysis of RNA Sequencing Data Using CLC Genomics Workbench

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Cited by 63 publications
(46 citation statements)
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“…COVID-19 RNA-seq Data: Quality Control (QC) Raw RNA-seq reads (Single-End) (FASTQ format) in quadruplicates were evaluated for quality using the CLC Genomics Workbench 20.0 (Qiagen, United States) as described previously (Ewing and Green, 1998;Liu and Di, 2020).…”
Section: Data Sourcementioning
confidence: 99%
“…COVID-19 RNA-seq Data: Quality Control (QC) Raw RNA-seq reads (Single-End) (FASTQ format) in quadruplicates were evaluated for quality using the CLC Genomics Workbench 20.0 (Qiagen, United States) as described previously (Ewing and Green, 1998;Liu and Di, 2020).…”
Section: Data Sourcementioning
confidence: 99%
“…Subsequently, sRNA reads were trimmed and assembled into larger contigs using CLC Genomic Workbench (Liu and Di 2020). These contigs almost covered the entire viral genome, whereas there were still some gaps with low coverage regions in the genome (Fig.…”
Section: Resultsmentioning
confidence: 99%
“…We carried out the quality assessment and read trimming of the RNA‐seq data using CLC Genomics Workbench 10 (QIAGENE) (Liu and Di ), with the following parameters: Minimum score to remove low‐quality sequences: 0.05. Maximum ambiguous nucleotides to remove: two nucleotides. Remove one nucleotide from 3′ end. Minimum sequence length: 15 nucleotides. …”
Section: Methodsmentioning
confidence: 99%
“…Genome scaffolds were constructed by de novo assembling of high‐quality reads from all samples using CLC Genomics Workbench 10 with default parameters (word size 20 and bubble size 50) (Liu and Di ). Clean reads were mapped to the obtained genome scaffolds using mismatch cost = 2, length fraction = 0.5 and similarity fraction = 0.8.…”
Section: Methodsmentioning
confidence: 99%