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Mappings are performed using a novel technique called revise and map, based on belief revision concepts.
The white light/PL images (bright field) and spatial PL spectral mappings are performed using a modified confocal microscope, equipped with a computer controlled XY stage, and a MMF (multimode fiber -coupled 410 nm diode laser.
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To accommodate possible biases of this read mapping approach, additional DNA and RNA-seq read mappings were performed with CLC Genomics Workbench v 6.5 (mapping parameters: minimum 90% of read aligned and minimum alignment identity 95%), and resulting polymorphisms compared.
ChIP-Seq Repeat Analysis For the repeat analysis of ChIP-seq profiles, the mappings were performed with the maq (mapping and assembly with qualities) aligner version 0.7.1 (Li et al., 2008 ).
The mappings were performed with and without SNP-tolerant mapping.
All mappings were performed in air at room temperature with relative humidity between 20% and 30%.
Elemental mappings were performed using an energy dispersive X-ray detector attached to the JEOL 2100F to measure the chemical composition of grown NWs.
Sequence read mappings were performed using CLC Genomics Workbench.
All mappings were performed in CLC Genomics Workbench 7.0.4 (CLC Bio Aarhus, Denmark).
Metabolic pathway mappings were performed using the KEGG Automatic Annotation Server [ 66].
All mappings were performed with Bismark (v.0.7.12; [ 35]) applying the parameters described above.
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