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The labelling module (Figure 1) is internally lead-shielded and situated on a standard workbench in the background environment.
Signal intensities from the generated images were measured and evaluated with Feature Extraction 10.10.11 and Agilent Genomic Standard Workbench Edition 6.5.0.58 (AGW6.5) software (Agilent) applying the Aberration Detection Method-2 (ADM-2) algorithm with a threshold of 6.0.
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Array data was analyzed with the Agilent Genomic Workbench Standard Edition 5.0 software.
The text files were then imported for analysis into Genomic Workbench, standard edition 5.0.14 (Agilent).
Then, Agilent Genomic Workbench Standard Edition 6.5 software (Agilent Technologies) was used to perform CNV interval detection.
The text files were then imported for analysis into Genomic Workbench, standard edition 6.5.0.58 (Agilent).
Examples are Metabolights in the United Kingdom, supported by the European COSMOS (COordination of Standards in MetabOlomicS) consortium that is developing metabolomics data standards, and Metabolomics Workbench, which aims to be the database for NIH-funded metabolomics projects.
The remaining reads were assembled de-novo using standard parameters in CLC Genomics workbench into 5,739 contigs with an average length of 771 bp.
BLASTn was performed in CLC Bio main Workbench 6.0 with standard settings: "word size" 11, "match" 1, "mismatch" −3, "gap cost existence" 5, "gap cost extension" 2. Bowtie(26) was applied to perform the alignment of the reads to the reference genomes (see parameters in the script in Supporting Information).
Self-alignment of the LTR-RT sequence was performed using CLC Genomics Workbench (V7.5) (http://www.clcbio.com/blog/clc-genomics-workbench-7-5/) with standard settings.
The current version of xQTL workbench can be linked to standard compute cluster software and includes R/qtl analysis, providing various QTL mapping methods like the new Multiple QTL Mapping [ 23].
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