One lane of 150 bp PE Illumina sequencing was performed from blood extracted genomic DNA from Dominette L1 014490 to generate 515 million reads (the SRA archive number in NCBI: SRP05124). Reads were mapped to assembly UMD3.1 using CLC Bio Genomics Workbench software (CLC Bio, Aarhus, Denmark; 85 % of the reads mapped to UMD3.1) using the following settings: mismatch cost = 2; linear gap cost for insertions and deletions = 3; length fraction = 0.6; similarity fraction = 0.9; auto detect pair distance and ignore non-specific matches.
Genomics workbench software
Manufactured by Qiagen
Sourced in Denmark, United States
Genomics Workbench software is a comprehensive bioinformatics platform designed for the analysis and interpretation of genomic data. It provides a suite of tools for tasks such as sequence alignment, variant calling, and functional annotation. The software is designed to facilitate efficient and effective data analysis for researchers and scientists working in the field of genomics.
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Lab products found in correlation
3 protocols using genomics workbench software
1
Bovine Whole Genome Sequencing
2
Metagenome Cellulase Identification
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The quality of the reads was checked with the FastQC package [22] and trimmed and filtered by quality using FASTX-ToolKit [23] . Sequences that mapped to the E. coli K12 genome and the pCC2FOS™ sequence (EU140752.1) were removed using Bowtie™ [24] . The de novo assembly of the reads was carried out with CLC™ Genomics Workbench software [25] . Cellulase sequences were identified by running a Basic Local Alignment Search Tool (Blastx) [26] (link) analysis against the non-redundant (nr) protein sequences database (parameters by default). The reads that showed identity over 75% to cellulase sequences were evaluated using Pfam [27] (link) to determine the family to which each hypothetical cellulase belongs.
3
RNA-Seq Analysis of Biopsied Tissues
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Fresh biopsies were stored in RNAlater until RNA was isolated using the miRNeasy kit (Qiagen, Valencia, Calif) following the manufacturer's instructions. From the total cohort, samples were selected based on their quality and quantity of RNA. From paired-end libraries, 20 million mappable 75-base-pair reads were acquired at the CCHMC DNA Sequencing and Genotyping Core Facility. Based on the Ensembl annotations, TopHat aligned data to GRCh37's human genome build. CLC Bio's Genomics Workbench software (Waltham, MA, USA) was used to analyze expression data using DESeq2.
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