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Gene identification in this complex genome must be achieved through deep transcriptome or genome sequencing, as well as experimental validation of expression.
For gene discovery and validation, we constructed EST library and performed sequencing as well as assembly as described in following section.
These variants were also analysed by Sanger DNA sequencing as a validation of the NGS method.
The scale of WES/WGS makes it prohibitive to evaluate all variants with alternative technologies and the cost limits the number of samples that can be sequenced as part of the validation process.
Once the ANN was trained, we tested the sensitivity and accuracy of the model to identify specific outcomes based on sequences presented as validation samples that were not used in the training process.
Two accessions called as reference and two accessions called as alternate were sequenced for validation.
The availability of large sets of annotated sequences as derived by identification, sequencing, and validation of genes expressed in the common bean will help in the development of an accurate and complete structural annotation of the common bean genome, a valid transcriptome map, and the identification of the genetic basis of agriculturally important traits in common bean.
SNVs and CNVs were validated by Sanger sequencing (93% validation rate) and genomic qPCR (96% validation rate), respectively.
MassARRAY genotyping results for this SNP were confirmed using an RFLP assay, as well as through Sanger sequencing validation of a subset of samples.
We have also provided evidence for single base resolution at the breakpoints, as indicated by Sanger sequencing validation of split-reads mappings (Additional files 2 and 3).
We therefore checked the methylation state of the ultrastable CpGs in the ENCODE reduced representation bisulfite sequencing (RRBS) data as validation.
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