The raw sequencing reads were trimmed, filtered and processed for a quality check using CLC Genomics Workbench (CLCBio, QIAGEN).1 The adaptors and raw reads with a quality score less than 0.05 (default setting, Phread 13, 95%) were removed. S. bebbiana reads were mapped to the closest high-quality genome available (Salix brachista C.K. Schneid., GCA_009078335.1_ASM907833v1) using CLCBio. The GenBank format file (*.gbff) was imported into CLCBio (as a track format) to get genomic and coding sequences (CDS) as a reference for the mapping. The number of mapped reads per gene (total exon reads per gene) was stored in the matrix format for further analyses.
Clc genomics workbench clcbio
Manufactured by Qiagen
The CLC Genomics Workbench is a software tool developed by CLCBio, a subsidiary of Qiagen. It is designed for analysis and visualization of genomic data. The core function of the CLC Genomics Workbench is to provide a comprehensive suite of tools for tasks such as read mapping, de novo assembly, variant calling, and data exploration.
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Lab products found in correlation
2 protocols using clc genomics workbench clcbio
1
Sequencing QC and Genome Mapping
2
Phylogenetic Analysis of Flowering Locus C Genes
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Illumina reads obtained after RNA-seq of 'nfc' and 'T15' were used for de novo assembly with Trinity (v.2.4.0) (Grabherr et al. 2011) (link). Contigs exhibiting high similarity (Blastn, expected value < 1e-150) with the cDNA sequences of BoFLC1a (XM_013756815.1), BoFLC1b (XM_013756817.1), BoFLC2 (AY306122.1), BoFLC3 (XM_013773027.1), and BoFLC5 (Bo3g024250.1) were selected. Phylogenetic analysis was performed using the selected contigs and BoFLC homologs, as well as the following B. napus FLC homologs derived from the C genome: BnaFLC.C02 (GSBRNA2T00068991001), BnaFLC.C03a (GSBRNA2T00134620001), BnaFLC.C03b (GSBRNA2T00024568001), BnaFLC.C09a (GSBRNA2T00016124001), and BnaFLC.C09b (GSBRNA2T00016119001). A phylogenetic tree was constructed using the Create Alignment and Create Tree (Algorithm = Neighbor Joining, Bootstrap = 1,000 replicates) function in CLC Genomics Workbench (CLC Bio; QIAGEN).
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